Genes and uses for plant enhancement

ABSTRACT

Transgenic seed for crops with enhanced agronomic traits are provided by trait-improving recombinant DNA in the nucleus of cells of the seed where plants grown from such transgenic seed exhibit one or more enhanced traits as compared to a control plant. Of particular interest are transgenic plants that have increased yield. The present invention also provides recombinant DNA molecules for expression of a protein, and recombinant DNA molecules for suppression of a protein.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 16/873,608, filed May 21, 2020, now U.S. Pat. No. 11,274,312, which is a continuation of U.S. application Ser. No. 15/732,766, filed Dec. 22, 2017, now U.S. Pat. No. 10,696,975, which is a continuation of U.S. application Ser. No 14/544,230, filed Dec. 10, 2014, now abandoned, which is a continuation of U.S. application Ser. No. 12/386,976, filed Apr. 24, 2009, now abandoned, which claims the benefit U.S. Provisional Application Ser. No. 61/125,908 filed on Apr. 29, 2008, all of which are hereby incorporated by reference in their entirety.

INCORPORATION OF SEQUENCE LISTING

Two copies of the sequence listing (Copy 1 and Copy 2) and a computer readable form (CRF) of the sequence listing, all on CD-Rs, each containing the file named 777052063104SUBSEQLIST.TXT, which is 319,329,870 bytes (measured in MS-WINDOWS) and recorded on CD-R on Aug. 30, 2022, are incorporated herein by reference in their entirety.

LENGTHY TABLES The patent application contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (https://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20230048751A1). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

INCORPORATION OF TABLES

The content of the following submission on ASCII text file is incorporated herein by reference in its entirety: a computer readable form (CRF) of Table 19 (file name: Table19.txt, date recorded: Aug. 30, 2022, size: 884,823 bytes).

FIELD OF THE INVENTION

Disclosed herein are recombinant DNA for providing enhanced traits to transgenic plants, seeds, pollen, plant cells and plant nucleui of such transgenic plants, methods of making and using such recombinant DNA, plants, seeds, pollen, plant cells and plant nuclei. Also disclosed are methods of producing hybrid seed comprising such recombinant DNA.

SUMMARY OF THE INVENTION

This invention provides recombinant DNA comprising polynucleotides characterized by SEQ ID NO: 1-803 and the cognate amino acid sequences of SEQ ID NO: 804-1606. The recombinant DNA is used for providing enhanced traits when stably integrated into the chromosomes and expressed in the nuclei of transgenic plants cells. In some aspects the recombinant DNA encodes a protein; in other aspects the recombinant DNA is transcribed to RNA that suppresses the expression of a native gene.

Such recombinant DNA in a plant cell nuclus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 20. Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 94617 through SEQ ID NO: 94734. In a particular aspect of the invention the recombinant DNA is characterized by its cognate amino, acid sequence that has at least 70% identity to any of SEQ ID NO: 804-1606.

This invention also provides transgenic plant cell nuclei comprising the recombinant DNA of the invention, transgenic plant cells comprising such nuclei, transgenic plants comprising a plurality of such transgenic plant cells, and transgenic seeds and transgenic pollen of such plants. Such transgenic plants are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA by screening transgenic plants for an enhanced trait as compared to control plants. The enhanced trait is one or more of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, enhanced seed protein and enhanced seed oil. Such recombinant DNA in a plant cell nuclus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 20. Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 94617 through SEQ ID NO: 94734.

In another aspect of the invention the plant cell nuclei, cells, plants, seeds, and pollen further comprise DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type plant cell.

This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA in the nucleus of the plant cells. More specifically the method comprises (a) screening a population of plants for an enhanced trait and recombinant DNA, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA; (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants and (c) collecting seed from a selected plant. Such method further comprises steps (a) verifying that the recombinant DNA is stably integrated in said selected plants; and (b) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by a recombinant DNA with a sequence of one of SEQ ID NO: 1-803; in one aspect of the invention the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and where the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound. In another aspect of the invention the plants are selected by identifying plants with the enhanced trait. The methods are used for manufacturing corn, soybean, cotton, canola, alfalfa, wheat, rice seed or any combinations thereof selected as having one of the enhanced traits described above.

Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA. The method further comprises producing corn plants from said hybrid corn seed, where a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.

Still other aspects of this invention relate to transgenic plants with enhanced water use efficiency or enhanced nitrogen use efficiency. For instance, this invention provides methods of growing a corn, cotton, soybean, or canola crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency. Alternatively methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop. This invention also provides methods of growing a corn, cotton, soybean or canola crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a plasmid map.

FIG. 2 illustrates a plasmid map.

FIG. 3 illustrates a plasmid map.

FIGS. 4A-4J illustrate a consensus amino acid sequence of SEQ ID NO: 1325 and its homologs. FIG. 4A illustrates the first part of the consensus amino acid sequence. FIG. 4B illustrates the second part of the consensus amino acid sequence. FIG. 4C illustrates the third part of the consensus amino acid sequence. FIG. 4D illustrates the fourth part of the consensus amino acid sequence. FIG. 4E illustrates the fifth part of the consensus amino acid sequence. FIG. 4F illustrates the sixth part of the consensus amino acid sequence. FIG. 4G illustrates the seventh part of the consensus amino acid sequence. FIG. 4H illustrates the eighth part of the consensus amino acid sequence. FIG. 4I illustrates the ninth part of the consensus amino acid sequence. FIG. 4J illustrates the tenth part of the consensus amino acid sequence.

DETAILED DESCRIPTION OF THE INVENTION

In the attached sequence listing:

SEQ ID NO: 1-803 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, where each represents a coding sequence for a protein;

SEQ ID NO: 804-1606 are amino acid sequences of the cognate protein of the “genes” with nucleotide coding sequence 1-803;

SEQ ID NO: 1607-94613 are amino acid sequences of homologous proteins;

SEQ ID NO: 94614 is a nucleotide sequence of a plasmid base vector for corn transformation; and

SEQ ID NO: 94615 is a DNA sequence of a plasmid base vector for soybean transformation.

SEQ ID NO: 94616 is a DNA sequence of a plasmid base vector for cotton transformation.

SEQ ID NO: 94617-94734 are consensus sequences.

Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.

TABLE 1 NUC SEQ ID CONSENSUS SEQ NO PEP SEQ ID NO GENE ID ID NO 5 808 CGPG1067 94617 6 809 CGPG1095 94618 7 810 CGPG1101 94619 8 811 CGPG1109 94620 10 813 CGPG1155 94621 12 815 CGPG1171 94622 13 816 CGPG1177 94623 19 822 CGPG1279 94624 20 823 CGPG1304 94625 22 825 CGPG1327 94626 57 860 CGPG1723 94627 78 881 CGPG1972 94628 88 891 CGPG2041 94629 90 893 CGPG2070 94630 98 901 CGPG2126 94631 99 902 CGPG213  94632 106 909 CGPG2193 94633 108 911 CGPG2224 94634 118 921 CGPG2319 94635 121 924 CGPG2359 94636 130 933 CGPG2408 94637 133 936 CGPG2414 94638 156 959 CGPG2863 94639 172 975 CGPG3183 94640 180 983 CGPG3280 94641 191 994 CGPG3405 94642 200 1003 CGPG3598 94643 202 1005 CGPG3606 94644 203 1006 CGPG3610 94645 204 1007 CGPG3620 94646 222 1025 CGPG3820 94647 226 1029 CGPG3958 94648 227 1030 CGPG3981 94649 236 1039 CGPG4083 94650 256 1059 CGPG4347 94651 257 1060 CGPG4354 94652 273 1076 CGPG4559 94653 294 1097 CGPG4802 94654 295 1098 CGPG4822 94655 296 1099 CGPG4826 94656 297 1100 CGPG4833 94657 298 1101 CGPG4841 94658 332 1135 CGPG5208 94659 393 1196 CGPG5750 94660 394 1197 CGPG5751 94661 413 1216 CGPG5922 94662 415 1218 CGPG5964 94663 432 1235 CGPG6137 94664 456 1259 CGPG6358 94665 501 1304 CGPG6803 94666 504 1307 CGPG6812 94667 506 1309 CGPG6827 94668 509 1312 CGPG6859 94669 514 1317 CGPG6886 94670 518 1321 CGPG6903 94671 520 1323 CGPG6933 94672 522 1325 CGPG6944 94673 523 1326 CGPG6949 94674 525 1328 CGPG6989 94675 527 1330 CGPG7003 94676 528 1331 CGPG7009 94677 531 1334 CGPG7062 94678 532 1335 CGPG7064 94679 534 1337 CGPG7109 94680 535 1338 CGPG7123 94681 538 1341 CGPG7159 94682 541 1344 CGPG7224 94683 569 1372 CGPG7505 94684 576 1379 CGPG7540 94685 582 1385 CGPG7568 94686 583 1386 CGPG7571 94687 584 1387 CGPG7587 94688 585 1388 CGPG7591 94689 588 1391 CGPG7633 94690 601 1404 CGPG7774 94691 602 1405 CGPG7777 94692 606 1409 CGPG7792 94693 613 1416 CGPG7851 94694 616 1419 CGPG7865 94695 622 1425 CGPG7934 94696 623 1426 CGPG7949 94697 624 1427 CGPG7954 94698 627 1430 CGPG7969 94699 641 1444 CGPG8072 94700 642 1445 CGPG8075 94701 644 1447 CGPG8100 94702 645 1448 CGPG8101 94703 646 1449 CGPG8104 94704 647 1450 CGPG8108 94705 648 1451 CGPG8116 94706 651 1454 CGPG8138 94707 654 1457 CGPG8163 94708 659 1462 CGPG8204 94709 662 1465 CGPG8234 94710 671 1474 CGPG8345 94711 686 1489 CGPG8515 94712 688 1491 CGPG8518 94713 690 1493 CGPG8523 94714 691 1494 CGPG8528 94715 693 1496 CGPG8553 94716 694 1497 CGPG8562 94717 697 1500 CGPG8589 94718 699 1502 CGPG8592 94719 703 1506 CGPG8648 94720 706 1509 CGPG8678 94721 707 1510 CGPG8694 94722 709 1512 CGPG8737 94723 710 1513 CGPG8745 94724 712 1515 CGPG8749 94725 715 1518 CGPG8781 94726 760 1563 CGPG9075 94727 762 1565 CGPG9094 94728 769 1572 CGPG9136 94729 770 1573 CGPG9156 94730 773 1576 CGPG9173 94731 781 1584 CGPG921  94732 788 1591 CGPG9281 94733 792 1595 CGPG9304 94734

The nuclei of this invention are identified by screening transgenic plants for one or more traits including enhanced drought stress tolerance, enhanced heat stress tolerance, enhanced cold stress tolerance, enhanced high salinity stress tolerance, enhanced low nitrogen availability stress tolerance, enhanced shade stress tolerance, enhanced plant growth and development at the stages of seed imbibition through early vegetative phase, and enhanced plant growth and development at the stages of leaf development, flower production and seed maturity.

“As used herein a “plant cell” means a plant cell that is transformed with stably-integrated, non-natural, recombinant DNA, e.g. by Agrobacterium-mediated transformation or by bombardment using microparticles coated with recombinant DNA or other means. A plant cell of this invention can be an originally-transformed plant cell that exists as a a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant DNA, or seed or pollen derived from a progeny transgenic plant.

As used herein a “transgenic plant” means a plant whose genome has been altered by the stable integration of recombinant DNA. A transgenic plant includes a plant regenerated from an originally-transformed plant cell and progeny transgenic plants from later generations or crosses of a transformed plant.

As used herein “recombinant DNA” means DNA which has been a genetically engineered and constructed outside of a cell including DNA containing naturally occurring DNA or cDNA or synthetic DNA.

As used herein a “homolog” means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention. Homologs are expressed by homologous genes. Homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a polynucleotide in the present invention can have any base sequence that has been changed from SEQ ID NO:1 through SEQ ID NO: 803 through substitution in accordance with degeneracy of the genetic code. Homologs are proteins that, when optimally aligned, have at least about 60% identity, about 70% or higher, at least about 80% and at least about 90% identity over the full length of a protein identified as being associated with imparting an enhanced trait when expressed in plant cells. Homologs include proteins with an amino acid sequence that has at least about 90% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.

Homologs are identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. A local sequence alignment program, e.g. BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism could be an ortholog or the only ortholog, a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit can be identified as an ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. A further aspect of the homologs encoded by DNA in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.

Homologous genes are genes which encode proteins with the same or similar biological function to the protein encoded by the second gene. Homologous genes can be generated by the event of speciation (see ortholog) or by the event of genetic duplication (see paralog). “Orthologs” refer to a set of homologous genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution; and “paralogs” refer to a set of homologous genes in the same species that have diverged from each other as a consequence of genetic duplication. Thus, homologous genes can be from the same or a different organism. As used herein, “homolog” means a protein that performs the same biological function as a second protein including those identified by sequence identity search.

As used herein, “percent identity” means the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, for example nucleotide sequence or amino acid sequence. An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components that are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence. “Percent identity” (“% identity”) is the identity fraction times 100. Such optimal alignment is understood to be deemed as local alignment of DNA sequences. For protein alignment, a local alignment of protein sequences should allow introduction of gaps to achieve optimal alignment. Percent identity is calculated over the aligned length not including the gaps introduced by the alignment per se.

As used herein, “promoter” means regulatory DNA for initializing transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell, e.g. is it well known that Agrobacterium promoters are functional in plant cells. Thus, plant promoters include promoter DNA obtained from plants, plant viruses and bacteria such as Agrobacterium and Bradyrhizobium bacteria. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters that initiate transcription only in certain tissues are referred to as “tissue specific”. A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that can effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter which is active under most conditions.

As used herein, “operably linked” refers to the association of two or more nucleic acid elements in a recombinant DNA construct, e.g. as when a promoter is operably linked with DNA that is transcribed to RNA whether for expressing or suppressing a protein. Recombinant DNA constructs can be designed to express a protein which can be an endogenous protein, an exogenous homologue of an endogenous protein or an exogenous protein with no native homologue. Alternatively, recombinant DNA constructs can be designed to suppress the level of an endogenous protein, e.g. by suppression of the native gene. Such gene suppression can be effectively employed through a native RNA interference (RNAi) mechanism in which recombinant DNA comprises both sense and anti-sense oriented DNA matched to the gene targeted for suppression where the recombinant DNA is transcribed into RNA that can form a double-strand to initiate-an RNAi mechanism. Gene suppression can also be effected by recombinant DNA that comprises anti-sense oriented DNA matched to the gene targeted for suppression. Gene suppression can also be effected by recombinant DNA that comprises DNA that is transcribed to a microRNA matched to the gene targeted for suppression. In the examples illustrating the invention recombinant DNA for effecting gene suppression that imparts is identified by the term “antisense”. It will be understood by a person of ordinary skill in the art that any of the ways of effecting gene suppression are contemplated and enabled by a showing of one approach to gene suppression.

As used herein “expressed” means produced, e.g. a protein is expressed in a plant cell when its cognate DNA is transcribed to mRNA that is translated to the protein.

As used herein “suppressed” means decreased, e.g. a protein is suppressed in a plant cell when there is a decrease in the amount and/or activity of the protein in the plant cell. The presence or activity of the protein can be decreased by any amount up to and including a total loss of protein expression and/or activity.

As used herein a “control plant” means a plant that does not contain the recombinant DNA that expressed a protein that imparts an enhanced trait. A control plant is to identify and select a transgenic plant that has an enhance trait. A suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, e.g. devoid of recombinant DNA. A suitable control plant can in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.

“Trait enhancement” means a detectable and desirable difference in a characteristic in a transgenic plant relative to a control plant or a reference. In some cases, the trait enhancement can be measured quantitatively. For example, the trait enhancement can entail at least about 2% difference in an observed trait, at least about 5% desirable difference, at least about about 10% difference, at least about about 20% difference, at least about 30% difference, at least about 40%, at least about 50% difference, at least about 60%, at least about 70% difference, at least about 80% difference, at least about 90% difference, or at least about a 100% difference, or an even greater difference. In other cases, the trait enhancement is only measured qualitatively. It is known that there can be a natural variation in a trait. Therefore, the trait enhancement observed entails a change of the normal distribution of the trait in the transgenic plant compared with the trait distribution observed in a control plant or a reference, which is evaluated by statistical methods provided herein. Trait enhancement includes, but is not limited to, yield increase, including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions can include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability, high plant density, or any combinations thereof.

“Yield” can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also be affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.

Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (e.g. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare. For example, maize yield can be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture. Increased yield can result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that could correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as can be manifest by alterations in the ratios of seed components.

“Stress condition” means a condition unfavorable for a plant, which adversely affect plant metabolism, growth and/or development A plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield. Specifically, “water deficit stress” used herein refers to the sub-optimal conditions for water and humidity needed for normal growth of natural plants. Relative water content (RWC) can be used as a physiological measure of plant water deficit. It measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. Conditions which can result in water deficit stress include, but are not limited to, heat, drought, high salinity and PEG induced osmotic stress.

“Cold stress” means the exposure of a plant to a temperatures below (two or more degrees Celsius below) those normal for a particular species or particular strain of plant.

“Nitrogen nutrient” means any one or any mix of the nitrate salts commonly used as plant nitrogen fertilizer, including, but not limited to, potassium nitrate, calcium nitrate, sodium nitrate, ammonium nitrate. The term ammonium as used herein means any one or any mix of the ammonium salts commonly used as plant nitrogen fertilizer, e.g., ammonium nitrate, ammonium chloride, ammonium sulfate, etc.

“Low nitrogen availability stress”, means a plant growth condition that does not contain sufficient nitrogen nutrient to maintain a healthy plant growth and/or for a plant to reach its typical yield under a sufficient nitrogen growth condition. For example, a limiting nitrogen condition can refers to a growth condition with 50% or less of the conventional nitrogen inputs. “Sufficient nitrogen growth condition” means a growth condition where the soil or growth medium contains or receives optimal amounts of nitrogen nutrient to sustain a healthy plant growth and/or for a plant to reach its typical yield for a particular plant species or a particular strain. One skilled in the art would recognize what constitute such soil, media and fertilizer inputs for most plant species.

“Shade stress” means a growth condition that has limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close, proximity of neighboring vegetation. Shade stress can become exacerbated when the planting density exceeds the average prevailing density for a particular plant species.

In some embodiments of the invention a constitutively active mutant, is constructed to achieve the desired effect. In other embodiments of the invention, a dominant negative gene is constructed to adversely affect the normal, wild-type gene product within the same cell.

DNA constructs are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait. Other construct components can include additional regulatory elements, such as 5′ leaders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.

Numerous promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens and the CaMV35S promoters from the cauliflower mosaic virus as disclosed in U.S. Pat. Nos. 5,164,316 and 5,322,938. Promoters derived from plant genes are found in U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Pat. No. 7,151,204, which discloses a maize chloroplast aldolase promoter and a maize aldolase (FDA) promoter, and U.S. Patent Application Publication 2003/0131377 A1, which discloses a maize nicotianamine synthase promoter, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.

In other aspects of the invention, preferential expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al. (1992) Plant Mol Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).

Furthermore, the promoters can be altered to contain multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with such constructs, the expression of the selected protein can be enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted upstream (5′) or downstream (3′) to the coding sequence. In some instances, these 5′ enhancing elements are introns. In one embodiment, enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876) and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.

In other aspects of the invention, sufficient expression in plant seed tissues is desired to affect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (-Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Per1) (Stacy et al. (1996) Plant Mol Biol. 31(6):1205-1216).

Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site. Well-known 3′ elements include those from Agrobacterium tumefaciens genes such as nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, tr7 3′, for example disclosed in U.S. Pat. No. 6,090,621, incorporated herein by reference; 3′ elements from plant genes such as wheat (Triticum aesevitum) heat shock protein 17 (Hsp17 3′), a wheat ubiquitin gene, a wheat fructose-1,6-biphosphatase gene, a rice glutelin gene, a rice lactate dehydrogenase gene and a rice beta-tubulin gene, all of which are disclosed in U.S. published patent application 2002/0192813 A1, incorporated herein by reference; and the pea (Pisum sativum) ribulose biphosphate carboxylase gene (rbs 3′), and 3′ elements from the genes within the host plant.

Constructs and vectors can also include a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides see U.S. Pat. Nos. 5,188,642 and 5,728,925, incorporated herein by reference. For description of the transit peptide region of an Arabidopsis EPSPS gene can be in the present invention, see Klee, H. J. et al (MGG (1987) 210:437-442).

Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein. Posttranscriptional gene suppression is mediated by transcription of RNA that forms double-stranded RNA (dsRNA) having homology to a gene targeted for suppression. Suppression can also be achieved by insertion mutations created by transposable elements can also prevent gene function. For example, in many dicot plants, transformation with the T-DNA of Agrobacterium can be readily achieved and large numbers of transformants can be rapidly obtained. Also, some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options. Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants can be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.

Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA can be further enhanced with stacked traits, e.g. a crop plant having an enhanced trait resulting from expression of DNA disclosed herein in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which transgenic plant tolerance has been demonstrated and the method of the present invention can be applied include, but are not limited to, glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides. Polynucleotide molecules encoding proteins involved in herbicide tolerance are well-known in the art and include, but are not limited to, a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos. 5,094,945; 5,627,061; 5,633,435 and 6,040,497 for imparting glyphosate tolerance; polynucleotide molecules encoding a glyphosate oxidoreductase (GOX) disclosed in U.S. Pat. No. 5,463,175 and a glyphosate-N-acetyl transferase (GAT) disclosed in U.S. Patent Application publication 2003/0083480 A1 also for imparting glyphosate tolerance; dicamba monooxygenase disclosed in U.S. Patent Application publication 2003/0135879 A1 for imparting dicamba tolerance; a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 for imparting bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crt1) described in Misawa et al, (1993) Plant J. 4:833-840 and in Misawa et al, (1994) Plant J. 6:481-489 for norflurazon tolerance; a polynucleotide molecule encoding acetohydroxyacid synthase (AHAS, aka ALS) described in Sathasiivan et al. (1990) Nucl. Acids Res. 18:2188-2193 for imparting tolerance to sulfonylurea herbicides; polynucleotide molecules known as bar genes disclosed in DeBlock, et al. (1987) EMBO J. 6:2513-2519 for imparting glufosinate and bialaphos tolerance; polynucleotide molecules disclosed in U.S. Patent Application Publication 2003/010609 A1 for imparting N-amino methyl phosphonic acid tolerance; polynucleotide molecules disclosed in U.S. Pat. No. 6,107,549 for impartinig pyridine herbicide resistance; molecules and methods for imparting tolerance to multiple herbicides such as glyphosate, atrazine, ALS inhibitors, isoxoflutole and glufosinate herbicides are disclosed in U.S. Pat. No. 6,376,754 and U.S. Patent Application Publication 2002/0112260, all of said U.S. Patents and Patent Application Publications are incorporated herein by reference. Molecules and methods for imparting insect/nematode/virus resistance are disclosed in U.S. Pat. Nos. 5,250,515; 5,880,275; 6,506,599; 5,986,175 and U.S. Patent Application Publication 2003/0150017 A1, all of which are incorporated herein by reference.

A “consensus amino acid sequence” means an artificial, amino acid sequence indicating conserved amino acids in the sequence of homologous proteins as determined by statistical analysis of an optimal alignment, e.g. CLUSTALW, of amino acid sequence of homolog proteins. The consensus sequences listed in the sequence listing were created by identifying the most frequent amino acid at each position in a set of aligned protein sequences. When there was 100% identity in an alignment the amino acid is indicated by a capital letter. When the occurance of an amino acid is at least about 70% in an alignment, the amino acid is indicated by a lower case letter. When there is no amino acid occurance of at least about 70%, e.g. due to diversity or gaps, the amino acid is indicated by an “x”. When used to defined embodiments of the invention, a consensus amino acid sequence will be aligned with a query protein amino acid sequence in an optimal alignment, e.g. CLUSTALW. An embodiment of the invention will have identity to the conserved amino acids indicated in the consensus amino acid sequence.

“Arabidopsis” means plants of Arabidopsis thaliana.

“Pfam” database is a large collection of multiple sequence alignments and hidden. Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. The Pfam database is currently maintained and updated by the Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the protein family alignments can be used for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.

A “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies. A Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function. The Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins. A Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.

Once one DNA is identified as encoding a protein which imparts an enhanced trait when expressed in transgenic plants, other DNA encoding proteins with the same Pfam domain module are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Models which characterizes the Pfam domains using HMMER software. Candidate proteins meeting the same Pfam domain module are in the protein family and have cognate DNA that is used in constructing recombinant DNA for the use in the plant cells of this invention.

Version 19.0 of the HMMER software and Pfam databases were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO: 804 through SEQ ID NO:1606. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 19 by Pfam analysis disclosed herein can be used in recombinant DNA of the plant cells of this invention, e.g. for selecting transgenic plants having enhanced agronomic traits. The relevant Pfam modules for use in this invention, as more specifically disclosed below, are Syntaxin::SNARE, Pro_isomerase, Pkinase, ATP-synt_G, Carboxyl_trans, CDC50, GATase::GMP_synt_C, F-box::WD40::WD40::WD40, dsrm::dsrm, Pyr_redox_2::Pyr_redox_dim, WAK::Pkinase, Pkinase_Tyr, PTPA, Biotin_lipoyl::E3_binding::2-oxoacid_dh, AAA, LRRNT_2::LRR_1::LRR_1::LRR_1, PRA1, TIM, YTH, ThiF, Hep_59, Pkinase, PALP::Thr_dehydrat_C::Thr_dehydrat_C, zf-Tim10_DDP, CAF1, Pkinase, Pyr_redox_2::Pyr_redox_dim, Response_reg, YIF1, NPH3, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase_Tyr, NOI, Fer2, AA_permease, Caleosin, IF4E, Pkinase, Ribul_P_3_epim, F-box::WD40::WD40::WD40::WD40::WD40::WD40, MIP, p450, Ribosomal_S5::Ribosomal_S5_C, Hpt, TBC, Acyltransferase, Epimerase, Pkinase, Dus, SelR, PH, Tyr-DNA_phospho, RRM_1, Pkinase, ECH, SRPRB, DUF599, Pkinase::efhand::efhand::efhand::efhand, ORC2, PMEI, p450, GLTP, Suc_Fer-like, CBS::CBS, ADH_N::ADH_zinc_N, LRRNT_2::LRR_1::LRR_1::LRR_1::Pkinase, F-box, adh_short, polyprenyl_synt, GHMP_kinases_N::GHMP_kinases_C, PsbW, Na_H_Exchanger::TrkA_C, Ribosomal_L12, CDC50, DCP1, Pyr_redox_2::Pyr_redox_dim, Steroid_dh, tRNA-synt_1 c::tRNA-synt_1c_C, Cupin_1::Cupin_1, peroxidase, Sugar_tr, Pro_isomerase, Iso_dh, PTS_2-RNA, Aminotran_5, ENOD93, KH_1::KH_1::KH_1::KH_1::KH_1, Mito_carr::Mito_carr::Mito_carr, DUF569::DUF569, C1_2::C1_2::C1_3::C1_2::C1_3::C1_2, DnaJ::zf-C2H2, Aldedh, AAA::Rep_fac_C, DUF641, Aminotran_1_2, TB2_DP1_HVA22, zf-C3HC4, RRM_1::RRM_2, Pkinase, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, Pyr_redox_2, IQ::IQ, SMP::SMP::SMP, AWPM-19, CLP_protease, Pkinase::NAF, PRMT5, PPR::PPR::PPR::PPR::PPR::PPR, Aldedh, ATP-synt_C::ATP-synt_C, adh_short, RCC1::RCC1::RCC1::RCC1::FYVE::DZC, p450, PfkB, PB1, Hexapep::Hexapep::Hexapep::Hexapep, Aminotran_1_2, DUF862, Aldedh, ADH_N::ADH_zinc_N, CDC48_N::AAA::AAA, AA_permease, UQ_con, Mem_trans, GFA, OPT, DUF887, Di19, U-box::Arm::Arm, DAO, G-alpha, Aminotran_3, 2OG-FeII_Oxy, Lectin_legB::Pkinase, NAC::UBA, efhand_like::PI-PLC-X::PI-PLC-Y::C2, TLC, ATP-grasp_2::Ligase_CoA, Pkinase, PRC::PRC, MFS_1::Sugar_tr, Copine::zf-C3HC4, RRM_1::RRM_1::RRM_1, Pribosyltran, AA_kinase, PhzC-PhzF, Gp_dh_N::Gp_dh_C, Sugar_tr, Pre-SET::SET, Alpha-amylase::Alpha-amyl_C2, Cyclin_N, FAE1_CUT1_RppA::ACP_syn_III_C, RPE65, efhand_like::PI-PLC-X::PI-PLC-Y::C2, Mito_carr::Mito_carr::Mito_carr, Invertase_neut, DSPc, LANC_like, Aminotran_5, Glutaminase, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, PGI, SSB, p450, La::RRM_1::RRM_3, Methyltransf_11, SBF, NTP_transferase::Hexapep::Hexapep::Hexapep, Mov34, Hydrolase, AAA, RRM_1::RRM_1, Pkinase::NAF, F-box::FBA_1, p450, F-box::LRR_2, zf-DHHC, TBP::TBP, DUF607, FMO-like, adh_short, ATP-synt_ab_N::ATP-synt_ab, RNase_PH, PP2C, UQ_con, Aminotran_1_2, p450, FMO-like, Gp_dh_N::Gp_dh_C, Mito_carr::Mito_carr::Mito_carr, zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH, GST_C, GH3, PAP_fibrillin, ThiF, Ribul_P_3_epim, DUF260, p450, MACPF, Steroid_dh, Response_reg, Carb_anhydrase, Aldedh, Pkinase, Methyltransf_11, PK::PK_C, Pkinase, DEK_C::SWIB::SWIB, TATA_RF, Tryp_alpha_amyl, Y_phosphatase2, TATA_RF, NifU_N, ENT, Pkinase, F-box::Kelch_2::Kelch_2, WD40::WD40, MtN3_slv::MtN3_slv, TB2_DP1_HVA22, Pkinase, Aldedh, AAA, Pyridoxa1_deC, zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC, Peptidase_M24, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, Arf, DUF1279, UPF0185, Rhodanese, adh_short, Tryp_alpha_amyl, Pkinase, UPF0139, CBS, Glyco_transf_29, iPGM_N::Metalloenzyme, Proteasome, Pkinase, UBX, ELFV_dehydrog_N::ELFV_dehydrog, p450, ADH N::ADH_zinc_N, zf-C3HC4, NDK, NAD_Gly3P_dh_N::NAD_Gly3P_dh_C, GlutR_N::Shikimate_DH::GlutR_dimer, p450, SNF5, p450, Pribosyltran, AIG1, Response_reg::CCT, mTERF, DUF220, Pkinase::NAF, zf-CCCH::zf-CCCH, Pkinase, Pkinase, MATH::MATH, Asparaginase, Pkinase, Gp_dh_N::Gp_dh_C, Pkinase, KH_1, Fcf1, PK::PK_C::PEP-utilizers, CRAL_TRIO_N::CRAL_TRIO, Raffinose_syn, DUF584, BT1, Aminotran_1_2, C1_2::C1_3::C1_3::C1_2::C1_3::C1_3::C1_2, FMO-like, PLAC8, F-box::Kelch_2::Kelch_1::Kelch_2, XS::XH, STT3, ABC_tran::ABC_tran, Aldo_ket_red, NTF2::RRM_1, DUF594, Biotin_lipoyl::2-oxoacid_dh, RRM_1, FHA, Mov34, MT-A70, Brix, X8, Auxin_inducible, Peptidase_M18, Sec61_beta, F-box::Kelch_1::Kelch_1, Brix, TIM, CTP_transf_1, Tetraspannin, PALP, DUF822, Pkinase, B3::B3, MFS_1, SFT2, F-box::Kelch_1::Kelch_1, DUF588, Thioredoxin, Alba, Ion_trans_2::Ion_trans_2, Peptidase_C48, YDG_SRA::Pre-SET::SET, Aldedh, Abhydrolase_3, p450, U-box::Arm::Arm::Arm::Arm, AA_permease, LAG1, peroxidase, PAD_porph, Pkinase, F-box, AIG2, p450, AARP2CN::DUF663, UPF0153, NAD_binding_2::6PGD, Pkinase, B_lectin::S_locus_glycop::PAN_1::Pkinase, EMP24_GP25L, DUF6::DUF6, DUF163, Sina, adh_short, Rho_GDI, zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC, VHS::GAT, Pyrophosphatase, DMRL_synthase, Cyclin_N::Cyclin_C, NDK, TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_C, SH3_1, UDPG_MGDP_dh_N::UDPG_MGDP_dh::UDPG_MGDP_dh_C, UIM::efhand, DUF579, Pkinase, DHBP_synthase::GTP_cyclohydro2, Peptidase_C14, Glycolytic, Pkinase, Lipase_3, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1, Snf7, BT1, PPDK_N::PEP-utilizers::PEP-utilizers_C, V-ATPase_G, RNA_pol_I_A49, Zip, WD40::WD40::WD40, Branch, RCC1::RCC1::RCC1::RCC1, TFIID-18kDa, Pkinase, Cullin, TFIID-31kDa, Asp, Pkinase, Ubie_methyltran, PPR::PPR, PPR::PPR::PPR::PPR::PPR::PPR::PPR, Fructosamin_kin, PPR::PPR::PPR::PPR::PPR::PPR, Pkinase_Tyr, p450, AA_permease, Glycos_transf_1, ECH::3HCDH_N::3HCDH, MIP, ADH_N::ADH_zinc_N, Aa_trans, DUF1517, Redoxin, RRS1, Pribosyltran, Sulfate_transp::STAS, DUF167, MMR_HSR1::DUF933, Aminotran_1_2, AA_permease, DUF620, Aldedh, Aminotran_1_2, LRR_1, CDP-OH_P_transf, DHBP_synthase::GTP_cyclohydro2, NHL::NHL, WD40::U3_snRNA_C, Na_sulph_symp, adh_short, Thioredoxin, Ribosomal_L7Ae, OTCace_N::OTCace, Mito_carr::Mito_carr::Mito_carr, Pescadillo_N::BRCT, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, mTERF, Chalcone, Per1, PPR::PPR, Na_H_Exchanger::TrkA_N, DEAD::Helicase_C, Cyclin_N::Cyclin_C, PP-binding, SRF-TF, SATase_N::Hexapep::Hexapep::Hexapep, PK::PK_C, adh_short, DUF6::DUF6, Pyr_redox_2, G-patch, WD40::WD40::WD40::WD40, G-alpha, VQ, WD40::WD40::WD40::WD40::WD40, Aminotran_3, Pribosyltran, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1, eIF3_subunit, H_PPase, Nodulin-like, Whi5, Tryp_alpha_amyl, NIR_SIR_ferr::NIR_SIR::NIR_SIR_ferr, RRM_1::RRM_1, Band_7, Asp, MFS_1, F420_oxidored, Pkinase, PRK, Na_Ca_ex::Na_Ca_ex, Bombesin, Pkinase, Epimerase, Pkinase, Inositol_P, Arm::Arm::Arm::Arm, PB1, Hin1, p450, RNA_pol_Rpb5_N::RNA_pol_Rpb5_C, Adap_comp_sub, Peptidase_M16::Peptidase_M16_C, Pkinase, PGK, Biotin_lipoyl::E3_binding::2-oxoacid_dh, Alg6_Alg8, F-box, MMR_HSR1, G6PD_N::G6PD_C, DAD, malic::Malic_M::PTA_PTB, ADH_N::ADH_zinc_N, LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1, PfkB, PA, Pyr_redox_2::Pyr_redox_dim, SIP1, PP2C, BT1, AhpC-TSA, GASA, Aminotran_3, Sad1_UNC, Pkinase, zf-MYND::PDCD2_C, Pkinase, PGK, ArfGap, GATase::GMP_synt_C, p450, DUF1637, 2OG-FeII_Oxy, Aldedh, DUF231, Glyco_transf_8, Sec1, DUF1475, Cellulose_synt, RRM_1::RRM_1::RRM_1, Usp, AA_permease, Acetyltransf_1::Bromodomain, Glyco_tran_28_C, RNA_pol_N, NTP_transferase, malic::Malic_M, Histone, Epimerase, UPF0061, ClpS, LEA_5, Auxin_inducible, PAP_fibrillin, Aldo_ket_red, Gln-synt_C, DREPP, p450, SFT2, eIF2A, Cenp-O, CPSase_sm_chain::GATase, WD40::WD40::WD40, Pkinase, Porin_3, Pkinase, Aminotran_1_2, GST_N::GST_C, F-box::Kelch_1::Kelch_1, IU_nuc_hydro, SYF2, PDT, Subtilisin_N::PA, Sugar_tr, WD40::WD40, p450, DUF829, Pyr_redox_2::Pyr_redox_dim, Aminotran_1_2, Cyclin_N::Cyclin_C, YgbB, Sugar_tr, SRF-TF, DUF231, DUF584, BT1, zf-C3HC4, Metallophos, FA_hydroxylase, p450, ACBP::Ank::Ank, LSM, SAM_1, LRR_1::LRR_1::Pkinase, Cullin, F-box::FBA_1, peroxidase, Rib_5-P_isom_A, zf-A20::zf-AN1, Dimerisation::Methyltransf_2, PGAM, PTR2, Copine, PALP, Exo_endo_phos, G6PD_N::G6PD_C, PLAC8, Aldo_ket_red, Ank::Ank, FBPase, zf-C3HC4, ACT::ACT, Suc_Fer-like, Pkinase_Tyr, G-alpha, RAMP4, Glutaredoxin, RRM_1::RRM_1, MT-A70, Response_reg::CCT, Arf, AP2, DUF177, 2OG-FeII_Oxy, LRRNT2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1, LRR_1, Aldedh, DUF1350, FAE1_CUT1_RppA::ACP_syn_III_C, Sybindin, zf-C3HC4, Nfu_N::NifU, Rho_GDI, PK::PK_C, NOSIC::Nop, PK::PK_C, PRK::Pribosyltran, PfkB, p450, DUF231, TFIID_30kDa, Aldedh, zf-AN1, GHMP_kinases_N::GHMP_kinases_C, DUF423, Pkinase, Cu-oxidase_3::Cu-oxidase::Cu-oxidase_2, PCI, RNase_PH::RNase_PH_C, DUF59, NTP_transferase, CH::EB1, Pkinase::Pkinase_C, DUF866, SMP::SMP::SMP, Aminotran_3, Transket_pyr::Transketolase_C, Copine, His_biosynth, Tbf5, DUF543, p450, C2, DUF616, Gp_dh_N::Gp_dh_C, Smg4_UPF3, DUF231, DUF89, WD40::WD40, Aldedh, ACT::ACT::ACT::ACT, Pkinase, Pyridoxa1_deC, Skp1_POZ::Skp1, NAP, FolB, p450, Pentapeptide::Pentapeptide, NTP_transferase::MannoseP_isomer, SQS_PSY, Cyclase, GASA, Rick_17kDa_Anti, FMO-like, B_lectin::S_locus_glycop::PAN_2, Peptidase_C12, Ribosomal_S6e, Glyoxalase, Response_reg::CCT, PHD::SET, Redoxin, G_glu_transpept, Synaptobrevin, p450, RALF, PALP, Branch, DUF579, Aminotran_3, Nramp, Enolase_N::Enolase_C, Str_synth, FAD_binding_3, MOSC_N::MOSC, Spc97_Spc98, Glycolytic, F-box::WD40::WD40::WD40::WD40, AA_kinase::ACT::ACT, RALF, and ATP_bind_1.

Plant Cell Transformation Methods

Numerous methods for transforming chromosomes in a plant cell nucleus with recombinant DNA are known in the art and are used in methods of preparing a transgenic plant cell nucleus cell, and plant. Two effective methods for such transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); U.S. Pat. No. 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean); U.S. Pat. No. 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn); U.S. Pat. No. 6,153,812 (wheat) and U.S. Pat. No. 6,365,807 (rice) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,463,174 (canola, also known as rapeseed); U.S. Pat. No. 5,591,616 (corn); U.S. Pat. No. 6,384,301 (soybean), 7,026,528 (wheat) and U.S. Pat. No. 6,329,571 (rice), all of which are incorporated herein by reference for enabling the production of transgenic plants. Transformation of plant material is practiced in tissue culture on a nutrient media, e.g. a mixture of nutrients that will allow cells to grow in vitro. Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. Callus can be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.

In addition to direct transformation of a plant material with a recombinant DNA, a transgenic plant cell nucleus can be prepared by crossing a first plant having cells with a transgenic nucleus with recombinant DNA with a second plant lacking the trangenci nucleus. For example, recombinant DNA can be introduced into a nucleus from a first plant line that is amenable to transformation to transgenic nucleus in cells that are grown into a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line. A transgenic plant with recombinant DNA providing an enhanced trait, e.g. enhanced yield, can be crossed with transgenic plant line having other recombinant DNA that confers another trait, for example herbicide resistance or pest resistance, to produce progeny plants having recombinant DNA that confers both traits. Typically, in such breeding for combining traits the transgenic plant donating the additional trait a male line and the transgenic plant carrying the base traits is the female line. The progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g. marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait. Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line

In practice, DNA is introduced into only a small percentage of target cell nuclei. Marker genes are used to provide an efficient system for identification of those cells with nuclei that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes. Some marker genes provide selective markers that confer resistance to a selective agent, such as an antibiotic or herbicide. Potentially transformed cells with a nucleus of the invention are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells can be tested further to confirm stable integration of the exogenous DNA in the nucleus. Explementary selective marker genes include those conferring resistance to antibiotics such as kanamycin (nptII), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate (EPSPS). Examples of such selectable markers are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference. Screenable markers which provide an ability to visually identify transformants can also be employed, e.g., a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known. It is also contemplated that combinations of screenable and selectable markers can be used for identification of transformed cells. See PCT publication WO 99/61129 (herein incorporated by reference) which discloses use of a gene fusion between a selectable marker gene and a screenable marker gene, e.g., an NPTII gene and a GFP gene.

Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, can be cultured in regeneration media and allowed to mature into plants. Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO₂, and 25-250 microeinsteins m⁻² s⁻¹ of light, prior to transfer, to a greenhouse or growth chamber for maturation. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue, and plant species. Plants can be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn. The regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.

Transgenic Plants and Seeds

Transgenic plants derived from transgenic plant cells having a transgenic nucleus of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention. Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait. For efficiency a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events. Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality. Of particular interest are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

To identify nuclei with recombinant DNA that confer enhanced traits to plants, Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.

Arabidopsis thaliana is used a model for genetics and metabolism in plants. A two-step screening process was employed which included two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait. The following Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.

Table 2 provides a list of protein encoding DNA (“genes”) as recombinant DNA for production of transgenic plants with enhanced agronomic trait, the elements of Table 2 are described by reference to:

PEP SEQ ID NO” identifies an amino acid sequence from SEQ ID NO: 804 to 1606.

“NUC SEQ ID NO” identifies a DNA sequence from SEQ ID NO:1 to 803

“construct_id” refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.

“Gene ID” refers to, an arbitrary name used to identify the particular DNA. “orientation” refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.

TABLE 2 NUC PEP SEQ SEQ ID ID Construct NO NO Gene ID ID Orientation  1  804 CGPG10 70244 SENSE  2  805 CGPG1008 71108 SENSE  3  806 CGPG1023 12816 SENSE  4  807 CGPG1038 12650 ANTI- SENSE  5  808 CGPG1067 12031 SENSE  6  809 CGPG1095 12217 SENSE  7  810 CGPG1101 12043 SENSE  8  811 CGPG1109 12147 ANTI- SENSE  9  812 CGPG1113 13638 ANTI- SENSE  10  813 CGPG1155 11860 ANTI- SENSE  11  814 CGPG1163 72361 SENSE  12  815 CGPG1171 12230 SENSE  13  816 CGPG1177 71626 SENSE  14  817 CGPG1205 13454 ANTI- SENSE  15  818 CGPG1207 12173 ANTI- SENSE  16  819 CGPG1215 17806 ANTI- SENSE  17  820 CGPG1223 12011 ANTI- SENSE  18  821 CGPG1250 72915 SENSE  19  822 CGPG1279 13231 SENSE  20  823 CGPG1304 13913 SENSE  21  824 CGPG1319 12749 ANTI- SENSE  22  825 CGPG1327 78901 SENSE  23  826 CGPG1329 75969 SENSE  24  827 CGPG133 15606 SENSE  25  828 CGPG1332 75946 SENSE  26  829 CGPG1343 13050 ANTI- SENSE  27  830 CGPG1348 75958 SENSE  28  831 CGPG1349 17333 SENSE  29  832 CGPG1373 76002 SENSE  30  833 CGPG1377 78735 SENSE  31  834 CGPG1412 13914 SENSE  32  835 CGPG1421 14405 SENSE  33  836 CGPG1426 75983 SENSE  34  837 CGPG1433 70721 ANTI- SENSE  35  838 CGPG1453 13811 SENSE  35  838 CGPG1453 13828 ANTI- SENSE  36  839 CGPG1454 13614 SENSE  37  840 CGPG1463. 76050 SENSE  38  841 CGPG1464 13038 ANTI- SENSE  39  842 CGPG1471 13040 ANTI- SENSE  40  843 CGPG1481 70716 ANTI- SENSE  40  843 CGPG1481 76039 SENSE  41  844 CGPG1499 71611 SENSE  42  845 CGPG150 70253 SENSE  43  846 CGPG1536 14415 SENSE  44  847 CGPG1539 13718 ANTI- SENSE  45  848 CGPG155 10706 ANTI- SENSE  45  848 CGPG155 10709 ANTI- SENSE  46  849 CGPG1583 14340 ANTI- SENSE  47  850 CGPG1588 13471 ANTI- SENSE  48  851 CGPG16 18304 SENSE  49  852 CGPG1609 13623 SENSE  50  853 CGPG1629 18302 SENSE  51  854 CGPG1637 15053 ANTI- SENSE  52  855 CGPG1653 15624 SENSE  53  856 CGPG1658 70412 SENSE  54  857 CGPG1663 17902 SENSE  55  858 CGPG1682 14272 ANTI- SENSE  56  859 CGPG1701 15122 SENSE  56  859 CGPG1701 70723 ANTI- SENSE  57  860 CGPG1723 14248 SENSE  58  861 CGPG1724 13965 ANTI- SENSE  59  862 CGPG1726 75912 SENSE  60  863 CGPG1736 14344 ANTI- SENSE  61  864 CGPG1741 14807 ANTI- SENSE  62  865 CGPG1783 17307 SENSE  63  866 CGPG1790 16431 ANTI- SENSE  64  867 CGPG1797 73075 SENSE  65  868 CGPG1845 16323 SENSE  66  869 CGPG1855 14833 ANTI- SENSE  67  870 CGPG1870 17030 ANTI- SENSE  68  871 CGPG1879 76414 SENSE  69  872 CGPG1886 16021 SENSE  70  873 CGPG1903 78701 SENSE  71  874 CGPG1905 78702 SENSE  72  875 CGPG1914 15220 ANTI- SENSE  73  876 CGPG193 15623 SENSE  74  877 CGPG1939 19402 SENSE  75  878 CGPG1949 70559 SENSE  76  879 CGPG1959 15111 ANTI- SENSE  77  880 CGPG197 70832 SENSE  78  881 CGPGI972 15129 SENSE  79  882 CGPG1981 76086 SENSE  80  883 CGPG1999 15203 ANTI- SENSE  81  884 CGPG2 70216 SENSE  82  885 CGPG2006 14910 ANTI- SENSE  83  886 CGPG2010 70318 SENSE  84  887 CGPG2011 15207 ANTI- SENSE  85  888 CGPG2014 14915 ANTI- SENSE  86  889 CGPG2023 15132 SENSE  87  890 CGPG2026 16229 SENSE  88  891 CGPG2041 14932 ANTI- SENSE  89  892 CGPG2064 76017 SENSE  90  893 CGPG2070 15964 ANTI- SENSE  91  894 CGPG2077 17227 SENSE  92  895 CGPG2095 72952 SENSE  93  896 CGPG2105 73706 SENSE  94  897 CGPG2108 18203 SENSE  95  898 CGPG2111 16309 SENSE  96  899 CGPG2124 15986 ANTI- SENSE  97  900 CGPG2125 15987 ANTI- SENSE  98  901 CGPG2126 16204 SENSE  99  902 CGPG213 11133 SENSE 100  903 CGPG2134 73977 SENSE 101  904 CGPG2139 15995 ANTI- SENSE 101  904 CGPG2139 18201 SENSE 102  905 CGPG2140 16887 SENSE 103  906 CGPG2153 16213 SENSE 104  907 CGPG2163 15507 ANTI- SENSE 105  908 CGPG2165 15508 ANTI- SENSE 106  909 CGPG2193 15959 ANTI- SENSE 107  910 CGPG2218 72427 ANTI- SENSE 108  911 CGPG2224 19041 ANTI- SENSE 109  912 CGPG2225 17802 SENSE 110  913 CGPG2229 19042 ANTI- SENSE 111  914 CGPG2243 76053 SENSE 112  915 CGPG2254 16120 SENSE 113  916 CGPG2268 15424 ANTI- SENSE 114  917 CGPG227 16401 SENSE 115  918 CGPG2312 72417 SENSE 116  919 CGPG2315 73702 SENSE 117  920 CGPG2316 70706 ANTI- SENSE 118  921 CGPG2319 71145 SENSE 119  922 CGPG235 11609 ANTI- SENSE 120  923 CGPG2358 71706 SENSE 121  924 CGPG2359 17325 SENSE 122  925 CGPG2361 70102 SENSE 123  926 CGPG2365 70106 SENSE 124  927 CGPG2372 70113 SENSE 125  928 CGPG2374 70115 SENSE 126  929 CGPG2377 70118 SENSE 127  930 CGPG2387 70128 SENSE 128  931 CGPG2389 70130 SENSE 129  932 CGPG2395 17103 ANTI- SENSE 130  933 CGPG2408 72748 SENSE 131  934 CGPG2409 17502 SENSE 132  935 CGPG2410 17503 SENSE 133  936 CGPG2414 78708 SENSE 134  937 CGPG2416 17504 SENSE 135  938 CGPG2441 17132 ANTI- SENSE 136  939 CGPG2450 72965 SENSE 137  940 CGPG2451 72796 SENSE 138  941 CGPG2492 16617 SENSE 139  942 CGPG2495 16640 SENSE 140  943 CGPG2506 16603 SENSE 141  944 CGPG2515 16612 SENSE 142  945 CGPG2531 16614 SENSE 143  946 CGPG2581 78354 SENSE 144  947 CGPG2584 17818 SENSE 145  948 CGPG2592 78370 SENSE 146  949 CGPG2612 70411 SENSE 147  950 CGPG2660 19154 SENSE 148  951 CGPG2663 19155 SENSE 149  952 CGPG2679 18307 SENSE 150  953 CGPG2696 72030 SENSE 151  954 CGPG2772 17916 SENSE 152  955 CGPG2773 17917 SENSE 153  956 CGPG281 17334 SENSE 154  957 CGPG2846 71531 SENSE 155  958 CGPG2852 18441 SENSE 156  959 CGPG2863 19162 SENSE 157  960 CGPG2870 73205 SENSE 158  961 CGPG2877 18306 SENSE 159  962 CGPG289 70808 SENSE 160  963 CGPG2924 17653 SENSE 161  964 CGPG2947 19535 SENSE 162  965 CGPG2963 71719 SENSE 163  966 CGPG2987 18546 SENSE 164  967 CGPG3033 19534 SENSE 165  968 CGPG3045 18421 SENSE 166  969 CGPG3046 18422 SENSE 167  970 CGPG3060 19539 SENSE 168  971 CGPG3075 19244 SENSE 169  972 CGPG310 15803 SENSE 170  973 CGPG3103 19545 SENSE 171  974 CGPG315 10222 ANTI- SENSE 171  974 CGPG315 72356 SENSE 172  975 CGPG3183 70425 SENSE 173  976 CGPG3189 19237 SENSE 174  977 CGPG3204 71303 SENSE 175  978 CGPG3208 19240 SENSE 176  979 CGPG3219 18535 SENSE 177  980 CGPG3233 19450 SENSE 178  981 CGPG3263 18221 SENSE 179  982 CGPG3276 18233 SENSE 180  983 CGPG3280 18236 SENSE 181  984 CGPG3282 18238 SENSE 182  985 CGPG3300 18309 SENSE 183  986 CGPG3318 70337 SENSE 184  987 CGPG3319 18319 SENSE 185  988 CGPG3326 70338 SENSE 186  989 CGPG333 10471 SENSE 187  990 CGPG3338 18331 SENSE 188  991 CGPG334 10228 ANTI- SENSE 188  991 CGPG334 10473 SENSE 189  992 CGPG3374 18261 SENSE 190  993 CGPG3402 18848 SENSE 191  994 CGPG3405 18268 SENSE 192  995 CGPG3413 18345 SENSE 193  996 CGPG3422 73607 SENSE 194  997 CGPG3436 18352 SENSE 195  998 CGPG3539 18357 SENSE 196  999 CGPG3550 19423 SENSE 197 1000 CGPG3551 78373 SENSE 198 1001 CGPG3552 70603 SENSE 199 1002 CGPG3572 19616 SENSE 200 1003 CGPG3598 19425 SENSE 201 1004 CGPG3599 19426 SENSE 202 1005 CGPG3606 18382 SENSE 203 1006 CGPG3610 71536 SENSE 204 1007 CGPG3620 70419 SENSE 205 1008 CGPG364 70827 SENSE 206 1009 CGPG3676 19311 SENSE 207 1010 CGPG3679 19323 SENSE 208 1011 CGPG3686 19320 SENSE 209 1012 CGPG3694 73613 SENSE 210 1013 CGPG3696 70432 SENSE 211 1014 CGPG3698 70433 SENSE 212 1015 CGPG3699 70434 SENSE 213 1016 CGPG3702 72614 SENSE 214 1017 CGPG3703 70436 SENSE 215 1018 CGPG3707 74226 SENSE 216 1019 CGPG3710 70439 SENSE 217 1020 CGPG3730 70446 SENSE 218 1021 CGPG3731 70613 SENSE 219 1022 CGPG3734 70447 SENSE 220 1023 CGPG3745 71725 SENSE 221 1024 CGPG3764 70462 SENSE 222 1025 CGPG3820 70545 SENSE 223 1026 CGPG3851 70741 SENSE 224 1027 CGPG3911 19702 SENSE 225 1028 CGPG3948 19985 SENSE 226 1029 CGPG3958 19775 SENSE 227 1030 CGPG3981 19829 SENSE 228 1031 CGPG3996 19982 SENSE 229 1032 CGPG4006 19755 SENSE 230 1033 CGPG4025 19732 SENSE 231 1034 CGPG4028 70365 SENSE 232 1035 CGPG403 10476 SENSE 233 1036 CGPG4041 19987 SENSE 234 1037 CGPG4078 19893 SENSE 235 1038 CGPG4079 19983 SENSE 236 1039 CGPG4083 19825 SENSE 237 1040 CGPG4092 19919 SENSE 238 1041 CGPG4104 19979 SENSE 239 1042 CGPG4127 19786 SENSE 240 1043 CGPG4135 70903 SENSE 241 1044 CGPG4161 70970 SENSE 242 1045 CGPG4180 70980 SENSE 243 1046 CGPG4191 70936 SENSE 244 1047 CGPG4199 71425 SENSE 245 1048 CGPG4241 78666 SENSE 246 1049 CGPG427 71202 SENSE 247 1050 CGPG4273 78973 SENSE 248 1051 CGPG4301 76411 SENSE 249 1052 CGPG4303 70635 SENSE 250 1053 CGPG4313 73715 SENSE 251 1054 CGPG4314 70638 SENSE 252 1055 CGPG4329 70642 SENSE 253 1056 CGPG4330 70643 SENSE 254 1057 CGPG4338 71564 SENSE 255 1058 CGPG4341 75039 SENSE 256 1059 CGPG4347 70653 SENSE 257 1060 CGPG4354 70655 SENSE 258 1061 CGPG4386 78321 SENSE 259 1062 CGPG4394 78307 SENSE 260 1063 CGPG4396 71808 SENSE 261 1064 CGPG4400 71810 SENSE 262 1065 CGPG4401 71313 SENSE 263 1066 CGPG441 72349 SENSE 264 1067 CGPG4413 71318 SENSE 265 1068 CGPG4427 71812 SENSE 266 1069 CGPG4446 74060 SENSE 267 1070 CGPG4448 71816 SENSE 268 1071 CGPG4474 71569 SENSE 269 1072 CGPG4482 70672 SENSE 270 1073 CGPG4511 71336 SENSE 271 1074 CGPG4517 71337 SENSE 272 1075 CGPG4551 71339 SENSE 273 1076 CGPG4559 71825 SENSE 274 1077 CGPG4567 73696 SENSE 275 1078 CGPG4586 70682 SENSE 276 1079 CGPG4600 70686 SENSE 277 1080 CGPG4631 78316 SENSE 278 1081 CGPG4642 71667 SENSE 279 1082 CGPG4645 71695 SENSE 280 1083 CGPG4646 71696 SENSE 281 1084 CGPG4649 72475 SENSE 282 1085 CGPG4653 71677 SENSE 283 1086 CGPG4656 71691 SENSE 284 1087 CGPG4668 72476 SENSE 285 1088 CGPG469 70803 SENSE 286 1089 CGPG4708 71612 SENSE 287 1090 CGPG4712 71637 SENSE 288 1091 CGPG4714 71629 SENSE 289 1092 CGPG4719 71622 SENSE 290 1093 CGPG473 70810 SENSE 291 1094 CGPG4734 72452 SENSE 292 1095 CGPG4736 74071 SENSE 293 1096 CGPG474 11042 SENSE 294 1097 CGPG4802 72510 SENSE 295 1098 CGPG4822 72537 SENSE 296 1099 CGPG4826 72541 SENSE 297 1100 CGPG4833 72617 SENSE 298 1101 CGPG4841 73755 SENSE 299 1102 CGPG4850 72630 SENSE 300 1103 CGPG4868 72645 SENSE 301 1104 CGPG4871 72647 SENSE 302 1105 CGPG488 14316 SENSE 303 1106 CGPG4908 73689 SENSE 304 1107 CGPG4913 73345 SENSE 305 1108 CGPG4921 73347 SENSE 306 1109 CGPG4954 73231 SENSE 307 1110 CGPG4956 78325 SENSE 308 1111 CGPG4959 72658 SENSE 309 1112 CGPG4965 72660 SENSE 310 1113 CGPG4970 72662 SENSE 311 1114 CGPG4980 73352 SENSE 312 1115 CGPG4982 72814 SENSE 313 1116 CGPG4985 72816 SENSE 314 1117 CGPG4990 72820 SENSE 315 1118 CGPG4991 73353 SENSE 316 1119 CGPG5007 75066 SENSE 317 1120 CGPG5015 78337 SENSE 318 1121 CGPG5026 73317 SENSE 319 1122 CGPG5029 73318 SENSE 320 1123 CGPG5046 73749 SENSE 321 1124 CGPG508 18704 SENSE 322 1125 CGPG5103 73221 SENSE 323 1126 CGPG511 71125 SENSE 324 1127 CGPG5121 76203 SENSE 325 1128 CGPG5126 75067 SENSE 326 1129 CGPG5136 73729 SENSE 327 1130 CGPG5146 75206 SENSE 328 1131 CGPG5149 73248 SENSE 329 1132 CGPG5181 73738 SENSE 330 1133 CGPG52 73332 SENSE 331 1134 CGPG5206 78335 SENSE 332 1135 CGPG5208 75821 SENSE 333 1136 CGPG5232 72038 SENSE 334 1137 CGPG5239 72027 SENSE 335 1138 CGPG5246 72016 SENSE 336 1139 CGPG525 70835 SENSE 337 1140 CGPG5268 72044 SENSE 338 1141 CGPG5272 72092 SENSE 339 1142 CGPG5333 72124 SENSE 340 1143 CGPG5338 72110 SENSE 341 1144 CGPG5341 73916 SENSE 342 1145 CGPG5369 74268 SENSE 343 1146 CGPG5372 74269 SENSE 344 1147 CGPG5380 77902 SENSE 345 1148 CGPG5386 74273 SENSE 346 1149 CGPG5396 74280 SENSE 347 1150 CGPG5397 74281 SENSE 348 1151 CGPG5421 74287 SENSE 349 1152 CGPG5433 73767 SENSE 350 1153 CGPG5439 77304 SENSE 351 1154 CGPG5453 73761 SENSE 352 1155 CGPG5456 74721 SENSE 353 1156 CGPG5483 74719 SENSE 354 1157 CGPG5492 74257 SENSE 355 1158 CGPG5508 72749 SENSE 356 1159 CGPG5520 72703 SENSE 357 1160 CGPG5525 72763 SENSE 358 1161 CGPG5526 72775 SENSE 359 1162 CGPG5530 72728 SENSE 360 1163 CGPG5534 72776 SENSE 361 1164 CGPG5537 72717 SENSE 362 1165 CGPG5545 72718 SENSE 363 1166 CGPG555 11715 SENSE 364 1167 CGPG5558 72779 SENSE 365 1168 CGPG5559 72791 SENSE 366 1169 CGPG5562 72732 SENSE 367 1170 CGPG5592 73027 SENSE 368 1171 CGPG5625 73058 SENSE 369 1172 CGPG5631 73126 SENSE 370 1173 CGPG5632 73138 SENSE 371 1174 CGPG5636 73174 SENSE 372 1175 CGPG5637 73186 SENSE 373 1176 CGPG564 11141 SENSE 374 1177 CGPG5641 73139 SENSE 375 1178 CGPG5650 73128 SENSE 376 1179 CGPG5653 73164 SENSE 377 1180 CGPG5657 73117 SENSE 378 1181 CGPG5671 73142 SENSE 379 1182 CGPG5672 73990 SENSE 380 1183 CGPG5677 73166 SENSE 381 1184 CGPG5678 73178 SENSE 382 1185 CGPG5679 73190 SENSE 383 1186 CGPG5682 73131 SENSE 384 1187 CGPG5691 73108 SENSE 385 1188 CGPG5699 73074 SENSE 386 1189 CGPG5705 73132 SENSE 387 1190 CGPG5722 73146 SENSE 388 1191 CGPG5734 73147 SENSE 389 1192 CGPG5736 73080 SENSE 390 1193 CGPG5744 73077 SENSE 391 1194 CGPG5747 73183 SENSE 392 1195 CGPG5748 73018 SENSE 393 1196 CGPG5750 73112 SENSE 394 1197 CGPG5751 73988 SENSE 395 1198 CGPG577 10908 ANTI- SENSE 395 1198 CGPG577 11147 SENSE 396 1199 CGPG5780 72909 SENSE 397 1200 CGPG5793 73987 SENSE 398 1201 CGPG5795 72922 SENSE / / / / / 399 1202 CGPG5796 73036 SENSE 400 1203 CGPG5800 72958 SENSE 401 1204 CGPG5812 77006 SENSE 402 1205 CGPG5815 74732 SENSE 403 1206 CGPG5838 74333 SENSE 404 1207 CGPG5844 74735 SENSE 405 1208 CGPG5846 74736 SENSE 406 1209 CGPG5851 74737 SENSE 407 1210 CGPG5857 76657 SENSE 408 1211 CGPG5862 76113 SENSE 409 1212 CGPG5863 74747 SENSE 410 1213 CGPG5867 77309 SENSE 411 1214 CGPG5872 74322 SENSE 412 1215 CGPG5913 76212 SENSE 413 1216 CGPG5922 76514 SENSE 414 1217 CGPG5961 75242 SENSE 415 1218 CGPG5964 77324 SENSE 416 1219 CGPG5968 74350 SENSE 417 1220 CGPG5984 77606 SENSE 418 1221 CGPG5991 76530 SENSE 419 1222 CGPG6006 76716 SENSE 420 1223 CGPG6015 77328 SENSE 421 1224 CGPG603 12204 SENSE 422 1225 CGPG6046 77011 SENSE 423 1226 CGPG6063 77607 SENSE 424 1227 CGPG6083 74612 SENSE 425 1228 CGPG6092 76126 SENSE 426 1229 CGPG6104 74376 SENSE 427 1230 CGPG6106 74377 SENSE 428 1231 CGPG6111 74381 SENSE 429 1232 CGPG6113 78364 SENSE 430 1233 CGPG6125 74623 SENSE 431 1234 CGPG6132 74668 SENSE 432 1235 CGPG6137 74629 SENSE 433 1236 CGPG6147 74635 SENSE 434 1237 CGPG6152 74638 SENSE 435 1238 CGPG6154 76721 SENSE 436 1239 CGPG6170 78365 SENSE 437 1240 CGPG6171 74655 SENSE 438 1241 CGPG6177 74660 SENSE 439 1242 CGPG6181 74661 SENSE 440 1243 CGPG6188 75259 SENSE 441 1244 CGPG6202 75282 SENSE 442 1245 CGPG6217 76724 SENSE 443 1246 CGPG623 12350 ANTI- SENSE 444 1247 CGPG6239 76522 SENSE 445 1248 CGPG6244 77903 SENSE 446 1249 CGPG6254 76653 SENSE 447 1250 CGPG6266 76524 SENSE 448 1251 CGPG627 11356 SENSE 449 1252 CGPG6271 75275 SENSE 450 1253 CGPG6278 76225 SENSE 451 1254 CGPG6288 75281 SENSE 452 1255 CGPG6309 74384 SENSE 453 1256 CGPG633 71238 SENSE 454 1257 CGPG635 12354 ANTI- SENSE 455 1258 CGPG6350 76236 SENSE 456 1259 CGPG6358 74682 SENSE 457 1260 CGPG6365 73425 SENSE 458 1261 CGPG6374 73438 SENSE 459 1262 CGPG6377 73474 SENSE 460 1263 CGPG638 70850 SENSE 461 1264 CGPG6397 73429 SENSE 462 1265 CGPG6398 73441 SENSE 464 1267 CGPG6415 73455 SENSE 465 1268 CGPG6421 73432 SENSE 466 1269 CGPG6442 73435 SENSE 467 1270 CGPG6443 77726 SENSE 468 1271 CGPG6446 73483 SENSE 469 1272 CGPG6453 73472 SENSE 470 1273 CGPG6466 73526 SENSE 471 1274 CGPG6467 73538 SENSE 472 1275 CGPG6470 73574 SENSE 473 1276 CGPG6475 73539 SENSE 474 1277 CGPG6477 73563 SENSE 475 1278 CGPG6478 73575 SENSE 476 1279 CGPG6493 73565 SENSE 477 1280 CGPG6506 73531 SENSE 478 1281 CGPG6518 73592 SENSE 479 1282 CGPG6546 74149 SENSE 480 1283 CGPG6556 74174 SENSE 481 1284 CGPG6562 74151 SENSE 482 1285 CGPG6566 74104 SENSE 483 1286 CGPG6571 74164 SENSE 484 1287 CGPG6576 74129 SENSE 485 1288 CGPG659 72340 SENSE 486 1289 CGPG6594 74155 SENSE 487 1290 CGPG6603 74168 SENSE 488 1291 CGPG6608 74133 SENSE 489 1292 CGPG6634 74160 SENSE 490 1293 CGPG6662 74485 SENSE 491 1294 CGPG6667 74450 SENSE 492 1295 CGPG6678 74487 SENSE 493 1296 CGPG6695 74406 SENSE 494 1297 CGPG6699 74454 SENSE 495 1298 CGPG670 11361 SENSE 496 1299 CGPG6705 74431 SENSE 497 1300 CGPG6735 74411 SENSE 498 1301 CGPG6744 74424 SENSE 499 1302 CGPG6753 74525 SENSE 500 1303 CGPG6757 74573 SENSE 501 1304 CGPG6803 75827 SENSE 502 1305 CGPG6806 77329 SENSE 503 1306 CGPG6811 77330 SENSE 504 1307 CGPG6812 75830 SENSE 505 1308 CGPG6815 75832 SENSE 506 1309 CGPG6827 75836 SENSE 507 1310 CGPG6830 77034 SENSE 508 1311 CGPG6839 76255 SENSE 509 1312 CGPG6859 76542 SENSE 510 1313 CGPG6864 77511 SENSE 511 1314 CGPG6877 76261 SENSE 512 1315 CGPG6878 78456 SENSE 513 1316 CGPG6880 77041 SENSE 514 1317 CGPG6886 76546 SENSE 515 1318 CGPG6887 75848 SENSE 516 1319 CGPG6895 77515 SENSE 517 1320 CGPG6896 76266 SENSE 518 1321 CGPG6903 75852 SENSE 519 1322 CGPG6912 76556 SENSE 520 1323 CGPG6933 77523 SENSE 521 1324 CGPG6942 75863 SENSE 522 1325 CGPG6944 77052 SENSE 523 1326 CGPG6949 75865 SENSE 524 1327 CGPG6969 76551 SENSE 525 1328 CGPG6989 76280 SENSE 526 1329 CGRG6991 75874 SENSE 527 1330 CGPG7003 75879 SENSE 528 1331 CGPG7009 75880 SENSE 529 1332 CGPG7037 77519 SENSE 530 1333 CGPG7051 76745 SENSE 531 1334 CGPG7062 76554 SENSE 532 1335 CGPG7064 76746 SENSE 533 1336 CGPG7086 76750 SENSE 534 1337 CGPG7109 76621 SENSE 535 1338 CGPG7123 76623 SENSE 536 1339 CGPG7136 76461 SENSE 537 1340 CGPG7147 76462 SENSE 538 1341 CGPG7159 78987 SENSE 539 1342 CGPG7186 76568 SENSE 540 1343 CGPG7222 76176 SENSE 541 1344 CGPG7224 76177 SENSE 542 1345 CGPG7233 78380 SENSE 543 1346 CGPG7238 76629 SENSE 544 1347 CGPG7253 76189 SENSE 545 1348 CGPG7255 76761 SENSE 546 1349 CGPG7286 78608 SENSE 547 1350 CGPG7292 78115 SENSE 548 1351 CGPG7301 74873 SENSE 549 1352 CGPG7305 74826 SENSE 550 1353 CGPG7307 74850 SENSE 551 1354 CGPG7318 74887 SENSE 552 1355 CGPG7319 74804 SENSE 553 1356 CGPG7345 74831 SENSE 554 1357 CGPG7368 74822 SENSE 555 1358 CGPG7385 74836 SENSE 556 1359 CGPG7391 74901 SENSE 557 1360 CGPG7405 74974 SENSE 558 1361 CGPG7415 74904 SENSE 559 1362 CGPG7416 74916 SENSE 560 1363 CGPG7420 74964 SENSE 561 1364 CGPG7432 74918 SENSE 562 1365 CGPG7436 74966 SENSE 563 1366 CGPG7445 74979 SENSE 564 1367 CGPG7465 74934 SENSE 565 1368 CGPG7473 77814 SENSE 566 1369 CGPG7489 75387 SENSE 567 1370 CGPG7492 75328 SENSE 568 1371 CGPG7499 77808 SENSE 569 1372 CGPG7505 75389 SENSE 570 1373 CGPG7507 75318 SENSE 571 1374 CGPG7508 75330 SENSE 572 1375 CGPG7509 75342 SENSE 573 1376 CGPG7511 75366 SENSE 574 1377 CGPG7515 75319 SENSE 575 1378 CGPG7521 75391 SENSE 576 1379 CGPG7540 75334 SENSE 577 1380 CGPG7547 75323 SENSE 578 1381 CGPG7561 75396 SENSE 579 1382 CGPG7562 75401 SENSE 580 1383 CGPG7563 75413 SENSE 581 1384 CGPG7567 75461 SENSE 582 1385 CGPG7568 75473 SENSE 583 1386 CGPG7571 77817 SENSE 584 1387 CGPG7587 75416 SENSE 585 1388 CGPG7591 75464 SENSE 586 1389 CGPG7597 75441 SENSE 587 1390 CGPG7606 75454 SENSE 588 1391 CGPG7633 75493 SENSE 589 1392 CGPG7637 75446 SENSE 590 1393 CGPG7649 75495 SENSE 591 1394 CGPG7658 75705 SENSE 592 1395 CGPG7664 77818 SENSE 593 1396 CGPG7666 75525 SENSE 594 1397 CGPG7668 75549 SENSE 595 1398 CGPG7742 75582 SENSE 596 1399 CGPG7746 75535 SENSE 597 1400 CGPG7747 75547 SENSE 598 1401 CGPG7752 75512 SENSE 599 1402 CGPG7766 75673 SENSE 600 1403 CGPG7770 75626 SENSE 601 1404 CGPG7774 75674 SENSE 602 1405 CGPG7777 75615 SENSE 603 1406 CGPG7778 75627 SENSE 604 1407 CGPG7786 75628 SENSE 605 1408 CGPG7788 75652 SENSE 606 1409 CGPG7792 75605 SENSE 607 1410 CGPG78 70228 SENSE 608 1411 CGPG783 13302 ANTI- SENSE 609 1412 CGPG7832 75610 SENSE 610 1413 CGPG7841 75623 SENSE 611 1414 CGPG7845 75671 SENSE 612 1415 CGPG7847 75695 SENSE 613 1416 CGPG7851 75648 SENSE 614 1417 CGPG7853 75672 SENSE 615 1418 CGPG7857 75713 SENSE 616 1419 CGPG7865 75714 SENSE 617 1420 CGPG7869 75762 SENSE 618 1421 CGPG7891 77954 SENSE 619 1422 CGPG7892 77955 SENSE 620 1423 CGPG7906 77541 SENSE 621 1424 CGPG7924 78131 SENSE 622 1425 CGPG7934 78134 SENSE 623 1426 CGPG7949 77554 SENSE 624 1427 CGPG7954 78992 SENSE 625 1428 CGPG7964 77557 SENSE 626 1429 CGPG7968 78128 SENSE 627 1430 CGPG7969 77560 SENSE 628 1431 CGPG7972 77561 SENSE 629 1432 CGPG7982 77958 SENSE 630 1433 CGPG7985 77563 SENSE 631 1434 CGPG7993 78994 SENSE 632 1435 CGPG8 74508 SENSE 633 1436 CGPG80 70229 SENSE 634 1437 CGPG8001 77959 SENSE 635 1438 CGPG8009 77567 SENSE 636 1439 CGPG802 11749 ANTI- SENSE 637 1440 CGPG8049 77578 SENSE 638 1441 CGPG806 11751 ANTI- SENSE 639 1442 CGPG8060 77963 SENSE 640 1443 CGPG8068 77925 SENSE 641 1444 CGPG8072 77927 SENSE 642 1445 CGPG8075 77345 SENSE 643 1446 CGPG81 70230 SENSE 644 1447 CGPG8100 77353 SENSE 645 1448 CGPG8101 77354 SENSE 646 1449 CGPG8104 77355 SENSE 647 1450 CGPG8108 77588 SENSE 648 1451 CGPG8116 77591 SENSE 649 1452 CGPG8125 77594 SENSE 650 1453 CGPG8134 77595 SENSE 651 1454 CGPG8138 77364 SENSE 652 1455 CGPG8156 78904 SENSE 653 1456 CGPG8159 77937 SENSE 654 1457 CGPG8163 77369 SENSE 655 1458 CGPG8179 77940 SENSE 656 1459 CGPG8193 78746 SENSE 657 1460 CGPG8197 77372 SENSE 658 1461 CGPG8198 78126 SENSE 659 1462 CGPG8204 77951 SENSE 660 1463 CGPG8211 75901 SENSE 661 1464 CGPG823 12123 ANTI- SENSE 662 1465 CGPG8234 75987 SENSE 663 1466 CGPG8238 75940 SENSE 664 1467 CGPG8260 75919 SENSE 665 1468 CGPG8267 75908 SENSE 666 1469 CGPG8268 75920 SENSE 667 1470 CGPG8274 75992 SENSE 668 1471 CGPG8277 75933 SENSE 669 1472 CGPG8279 77965 SENSE 670 1473 CGPG8284 77966 SENSE 671 1474 CGPG8345 77972 SENSE 672 1475 CGPG8408 78522 SENSE 673 1476 CGPG842 12194 ANTI- SENSE 674 1477 CGPG8421 78525 SENSE 675 1478 CGPG8435 78527 SENSE 676 1479 CGPG8440 78917 SENSE 677 1480 CGPG8453 78920 SENSE 678 1481 CGPG8470 78535 SENSE 679 1482 CGPG8479 78538 SENSE 680 1483 CGPG8489 78922 SENSE 681 1484 CGPG8498 77984 SENSE 682 1485 CGPG85 73938 SENSE 683 1486 CGPG8501 78621 SENSE 684 1487 CGPG8507 77990 SENSE 685 1488 CGPG8509 78386 SENSE 686 1489 CGPG8515 78001 SENSE 687 1490 CGPG8517 78543 SENSE 688 1491 CGPG8518 78002 SENSE 689 1492 CGPG852 12259 SENSE 690 1493 CGPG8523 78005 SENSE 691 1494 CGPG8528 78008 SENSE 692 1495 CGPG8552 78019 SENSE 693 1496 CGPG8553 78020 SENSE 694 1497 CGPG8562 78023 SENSE 695 1498 CGPG8567 78548 SENSE 696 1499 CGPG8580 78161 SENSE 697 1500 CGPG8589 78162 SENSE 698 1501 CGPG8590 78033 SENSE 699 1502 CGPG8592 78622 SENSE 700 1503 CGPG8594 78036 SENSE 701 1504 CGPG8606 78043 SENSE 702 1505 CGPG8628 78165 SENSE 703 1506 CGPG8648 78066 SENSE 704 1507 CGPG8654 78069 SENSE 705 1508 CGPG8668 78183 SENSE 706 1509 CGPG8678 78170 SENSE 707 1510 CGPG8694 78953 SENSE 708 1511 CGPG8702 78929 SENSE 709 1512 CGPG8737 78564 SENSE 710 1513 CGPG8745 78566 SENSE 711 1514 CGPG8748 78591 SENSE 712 1515 CGPG8749 78181 SENSE 713 1516 CGPG8770 78190 SENSE 714 1517 CGPG8777 78571 SENSE 715 1518 CGPG8781 78933 SENSE 716 1519 CGPG8786 78573 SENSE 717 1520 CGPG8792 78632 SENSE 718 1521 CGPG8801 78959 SENSE 719 1522 CGPG8809 78191 SENSE 720 1523 CGPG8840 78595 SENSE 721 1524 CGPG8850 78646 SENSE 722 1525 CGPG8870 76325 SENSE 723 1526 CGPG8871 76337 SENSE 724 1527 CGPG8872 76349 SENSE 725 1528 CGPG8876 76302 SENSE 726 1529 CGPG8902 76329 SENSE 727 1530 CGPG8904 76353 SENSE 728 1531 CGPG8907 76389 SENSE 729 1532 CGPG8914 76378 SENSE 730 1533 CGPG8931 76392 SENSE 731 1534 CGPG8933 76321 SENSE 732 1535 CGPG8935 76345 SENSE 733 1536 CGPG8938 76381 SENSE 734 1537 CGPG8944 76358 SENSE 735 1538 CGPG895 12629 SENSE 736 1539 CGPG8950 76335 SENSE 737 1540 CGPG8961 76372 SENSE 738 1541 CGPG8963 76396 SENSE 739 1542 CGPG898 72314 SENSE 740 1543 CGPG8993 77840 SENSE 741 1544 CGPG8994 76886 SENSE 742 1545 CGPG8995 76803 SENSE 743 1546 CGPG90 10302 ANTI- SENSE 744 1547 CGPG900 71107 SENSE 745 1548 CGPG9002 76887 SENSE 746 1549 CGPG9009 77842 SENSE 747 1550 CGPG9011 76805 SENSE 748 1551 CGPG9012 76817 SENSE 749 1552 CGPG9017 77843 SENSE 750 1553 CGPG9025 77844 SENSE 751 1554 CGPG9026 76890 SENSE 752 1555 CGPG9032 77839 SENSE 753 1556 CGPG9040 76868 SENSE 754 1557 CGPG9044 76821 SENSE 755 1558 CGPG9048 76869 SENSE 756 1559 CGPG9049 76881 SENSE 757 1560 CGPG9058 76894 SENSE 758 1561 CGPG906 11930 ANTI- SENSE 759 1562 CGPG9070 76848 SENSE 760 1563 CGPG9075 76901 SENSE 761 1564 CGPG9084 76914 SENSE 762 1565 CGPG9094 76939 SENSE 763 1566 CGPG9098 76987 SENSE 764 1567 CGPG9099 76904 SENSE 765 1568 CGPG9110 76941 SENSE 766 1569 CGPG9119 77113 SENSE 767 1570 CGPG9125 77185 SENSE 768 1571 CGPG913 12911 SENSE 769 1572 CGPG9136 77127 SENSE 770 1573 CGPG9156 77177 SENSE 771 1574 CGPG9164 77178 SENSE 772 1575 CGPG9172 77179 SENSE 773 1576 CGPG9173 77191 SENSE 774 1577 CGPG9185 77145 SENSE 775 1578 CGPG9187 77169 SENSE 776 1579 CGPG9190 77110 SENSE 777 1580 CGPG9193 77146 SENSE 778 1581 CGPG9195 77170 SENSE 779 1582 CGPG9203 77171 SENSE 780 1583 CGPG9209 77148 SENSE 781 1584 CGPG921 11933 ANTI- SENSE 782 1585 CGPG9210 77160 SENSE 783 1586 CGPG9211 77172 SENSE 784 1587 CGPG9212 77184 SENSE 785 1588 CGPG9216 77225 SENSE 786 1589 CGPG9226 77250 SENSE 787 1590 CGPG9252 77277 SENSE 788 1591 CGPG9281 77245 SENSE 789 1592 CGPG9289 77246 SENSE 790 1593 CGPG9298 77462 SENSE 791 1594 CGPG9299 77414 SENSE 792 1595 CGPG9304 77439 SENSE 793 1596 CGPG9310 77463 SENSE 794 1597 CGPG9316 77488 SENSE 795 1598 CGPG9317 77441 SENSE 796 1599 CGPG9318 77464 SENSE 797 1600 CGPG9324 77442 SENSE 798 1601 CGPG9357 77419 SENSE 799 1602 CGPG965 12444 SENSE 800 1603 CGPG970 11791 ANTI- SENSE 800 1603 CGPG970 12445 SENSE 801 1604 CGPG982 71249 SENSE 802 1605 CGPG994 71237 SENSE 803 1606 CGPG996 12315 ANTI- SENSE 803 1606 CGPG996 12366 SENSE

Recombinant DNA

DNA for use in the present invention to improve traits in plants have a nucleotide sequence of SEQ ID NO:1 through SEQ ID NO:803, as well as the homologs of such DNA molecules. A subset of the DNA for gene suppression aspects of the invention includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of 21 or more consecutive nucleotides. In some embodiments, the nucleotides for gene suppression can be 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more consecutive nucleotides. Oligonucleotides having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 803 can be as probes and primers for detection of the polynucleotides used in the invention. Other embodiments this invention are variants of the DNA. Such variants can be naturally occurring, including DNA from homologous genes from the same or a different species, or can be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a DNA in the present invention can have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.

Homologs of the genes providing DNA demonstrated uses in improving traits in model plants disclosed herein will generally have significant identity with the DNA disclosed herein. DNA is substantially identical to a reference DNA if, when the sequences of the polynucleotides are optimally aligned there is about 60% nucleotide equivalence; about 70% equivalence; about 80% equivalence; about 85% equivalence; about 90%; about 95%; about 98%, about 99% equivalence or about 99.5 equivalence over a comparison window. A comparison window can be at least 50-100 nucleotides or the entire length of the polynucleotide provided herein. Optimal alignment of sequences for aligning a comparison window can be conducted by algorithms; for example by computerized implementations of these algorithms (such as, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference polynucleotide can be a full-length molecule or a portion of a longer molecule. In one embodiment, the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.

Proteins used for imparting enhanced traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins used for generation of transgenic plants having enhanced traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606, as well as homologs of such proteins.

Homologs of the proteins in the invention are identified by comparison of the amino acid sequence of the protein to amino acid sequences of proteins from the same or different plant sources, e.g., manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. As used herein, a homolog is a protein from the same or a different organism that performs the same biological function as the polypeptide to which it is compared. An orthologous relation between two organisms is not necessarily manifest as a one-to-one correspondence between two genes, because a gene can be duplicated or deleted after organism phylogenetic separation, such as speciation. For a given protein, there can be no ortholog or more than one ortholog. Other complicating factors include alternatively spliced transcripts from the same gene, limited gene identification, redundant copies of the same gene with different sequence lengths or corrected sequence. A local sequence alignment program, e.g., BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism could be an ortholog or the only ortholog, a reciprocal BLAST search is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. Thus, homolog is used herein to describe proteins that are assumed to have functional similarity by inference from sequence base similarity. The relationship of homologs with amino acid sequences of SEQ ID NO: 1607 to SEQ ID NO: 94613 to the proteins with amino acid sequences of SEQ ID NO: 804 to SEQ ID NO: 1606 are found in the listing of Table 19.

Other functional homolog proteins differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine. Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs. Representative amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. Conserved substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the invention comprises proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.

Homologs of the trait-improving proteins provided herein will generally demonstrate significant sequence identity. Of particular interest are proteins having at least about 50% sequence identity, at least about 70% sequence identity or higher, e.g., at least about 80% sequence identity with an amino acid sequence of SEQ ID NO: 804 to SEQ ID NO: 1606. Additional embodiments also include those with higher identity, e.g., about 90%, about 92.5%, about 95%, about 98%, about 99%, or to about 99.5% identity. Identity of protein homologs is determined by optimally aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison. The window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 804 to SEQ ID NO: 1606.

Genes that are homologous to each other can be grouped into families and included in multiple sequence alignments. Then a consensus sequence for each group can be derived. This analysis enables the derivation of conserved and class- (family) specific residues or motifs that are functionally important. These conserved residues and motifs can be further validated with 3D protein structure if available. The consensus sequence can be used to define the full scope of the invention, e.g., to identify proteins with a homolog relationship. Thus, the present invention contemplates that protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.

Discovery of Trait-Improving Recombinant DNA

To identify nuclei with recombinant DNA that confer enhanced traits to plants, Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.

Arabidopsis thaliana is used a model for genetics and metabolism in plants. Arabidopsis has a small genome, and well-documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz, et al., Methods in Arabidopsis Research et al., (1992), World Scientific, New Jersey, New Jersey, in “Preface”).

A two-step screening process was employed which comprised two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait. The following Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.

In particular, Table 3 reports:

“PEP SEQ ID” which is the amino acid sequence of the protein cognate to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.

“construct_id” is an arbitrary name for the recombinant DNA describe more particularly in Table 1.

“annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.

“description” refers to the description of the top BLAST hit.

“e-value” provides the expectation value for the BLAST hit.

“% id” refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.

“traits” identify by two letter codes the confirmed enhancement in a transgenic plant provided by the recombinant DNA. The codes for enhanced traits are:

“CK” which indicates cold tolerance enhancement identified under a cold shock tolerance screen;

“CS” which indicates cold tolerance enhancement identified by a cold germination tolerance screen;

“DS” which indicates drought tolerance enhancement identified by a soil drought stress tolerance screen;

“PEG” which indicates osmotic stress tolerance enhancement identified by a PEG induced osmotic stress tolerance screen;

“HS” which indicates heat stress tolerance enhancement identified by a heat stress tolerance screen;

“SS” which indicates high salinity stress tolerance enhancement identified by a salt stress tolerance screen;

“LN” which indicates nitrogen use efficiency enhancement identified by a limited nitrogen tolerance screen;

“LL” which indicates attenuated shade avoidance response identified by a shade tolerance screen under a low light condition;

“PP” which indicates enhanced growth and development at early stages identified by an early plant growth and development screen;

“SP” which indicates enhanced growth and development at late stages identified by a late plant growth and development screen provided herein.

TABLE 3 PEP ID Annotation NO % SEQ Construct E-value Id Description traits 804 70244 0 95 ref|NP_193113.1|CYP83A1 (CYTOCHROME P450 83A1); HS oxygen binding [Arabidopsis thaliana] 805 71108 3.00E−54 100 gb|AAB61093.1|F20P5.4 gene product [Arabidopsis LL thaliana] 806 12816 0 79 ref|NP_190754.2|CAX3 (cation exchanger 3); cation:cation LN antiporter [Arabidopsis thaliana] 807 12650 1.00E−159 89 gb|AAC25513.1|AAC25513 Strong similarity to hypothetical LN protein gb|Y09823| from A. thaliana. 808 12031 1.00E−56 88 ref|NP_179413.1|unknown protein [Arabidopsis thaliana] LN 809 12217 1.00E−168 88 ref|NP_194233.1|unknown protein [Arabidopsis thaliana] LN 810 12043 2.00E−46 100 ref|NP_194730.1|unknown protein [Arabidopsis thaliana] PP 811 12147 2.00E−33 68 ref|NP_190718.1|unknown protein [Arabidopsis thaliana] LN 812 13638 0 100 ref|NP_189940.1|unknown protein [Arabidopsis thaliana] DS 813 11860 2.00E−81 93 ref|NP_973419.1|unknown protein [Arabidopsis thaliana] LN 814 72361 1.00E−139 93 ref|NP_178534.2|IBR5 (INDOLE−3-BUTYRIC ACID CK RESPONSE 5); protein tyrosine/serine/threonine phosphatase [Arabidopsis thaliana] 815 12230 1.00E−23 100 ref|NP_564545.1|TOM6 (TRANSLOCASE OF THE LN OUTER MITOCHONDRIAL MEMBRANE 6) [Arabidopsis thaliana] sp|Q9XIA7|TOM6_ARATH Mitochondrial import receptor subunit TOM6 homolog (Translocase of outer membrane 6 kDa subunit homolog) 816 71626 1.00E−47 93 ref|NP_177455.1|unknown protein [Arabidopsis thaliana] CK 817 13454 0 96 ref|NP_566136.1|armadillo/beta-catenin repeat family LN protein [Arabidopsis thaliana] 818 12173 4.00E−49 100 ref|NP_186751.1|ATISU2/ISU2 (IscU-like 2); structural CK molecule [Arabidopsis thaliana] 819 17806 1.00E−35 54 ref|NP_188341.2|unknown protein [Arabidopsis thaliana] LN 820 12011 1.00E−144 99 ref|NP_567393.1|ATP-binding family protein [Arabidopsis LN thaliana] 821 72915 1.00E−135 77 sp|Q94A43|BEH2_ARATHBES1/BZR1 homolog protein 2 SS 822 13231 1.00E−161 96 ref|NP_178361.2|nucleic acid binding [Arabidopsis HS thaliana] 823 13913 1.00E−147 88 ref|NP_028242.1|PDV2 (PLASTID D1VIS1ON2) HS [Arabidopsis thaliana] gb|AAD26950.1| expressed protein [Arabidopsis thaliana] 824 12749 1.00E−140 100 ref|NP_196620.1|unknown protein [Arabidopsis thaliana] LN 825 78901 0 97 ref|NP_565919.1(COI1 (CORONATINE INSENSITIVE 1); HS PP ubiquitin-protein ligase [Arabidopsis thaliana] 826 75969 0 100 ref|NP_174005.1|ATCUL3/ATCUL3A/CUL3/CUL3A (Cullin CS HS 3A); protein binding/ubiquitin-protein ligase [Arabidopsis thaliana] 827 15606 0 96 gb|AAA32781.1|cyclin emb|CAA44169.1| cyclin HS [Arabidopsis thaliana] 828 75946 0 96 ref|NP_171797.2|CUL2 (cullin 2) [Arabidopsis thaliana] LL 829 13050 0 97 ref|NP_175955.1|F-boxfamily protein [Arabidopsis LN thaliana] 830 75958 0 94 ref|NP_177170.1|lectin protein kinase, putative HS LN [Arabidopsis thaliana] 831 17333 0 93 gb|AAF02796.1|AF195115_16 Similar to receptor-like PP protein kinase precusor; F5I10.19 [Arabidopsis thaliana] 832 76002 0 100 ref|NP_193038.1|MHK; kinase [Arabidopsis thaliana] HS PEG sp|P43294|MHK_ARATH Serine/threonine-protein kinase MHK 833 78735 0 94 ref|NP_187132.1|protein kinase, putative [Arabidopsis LL PEG thaliana] 834 13914 0 100 ref|NP_195033.1|pyruvate decarboxylase, putative HS SS [Arabidopsis thaliana] 835 14405 0 92 ref|NP_187341.1|DIN3/LTA1 (DARK INDUCIBLE 3); LN SP alpha-ketoacid dehydrogenase [Arabidopsis thaliana] 836 75983 0 100 ref|NP_171655.1|ACS2 (1-Amino-cyclopropane-1- CK carboxylate synthase 2) [Arabidopsis thaliana] 837 70721 0 94 ref|NP_851005.1|LPD2 (LIPOAMIDE DEHYDROGENASE HS LN 2); FAD, binding/dihydrolipoyl dehydrogenase/ disulfide oxidoreductase/oxidoreductase [Arabidopsis thaliana] 838 13811 0 92 ref|NP_178093.1|ATNADP-ME4 (NADP-MALIC ENZYME DS 4); malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)/malic enzyme/oxidoreductase, acting on NADH or NADPH, NAD or NADP as acceptor [Arabidopsis thaliana] 838 13828 0 92 ref|NP_178093.1|ATNADP-ME4 (NADP-MALIC ENZYME LN 4); malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)/malic enzyme/oxidoreductase, acting on NADH or NADPH, NAD or NADP as acceptor [Arabidopsis thaliana] 839 13614 1.00E−122 96 ref|NP_176518.1|ribulose-phosphate 3-epimerase, LN cytosolic, putative/pentose-5-phosphate 3-epimerase, putative [Arabidopsis thaliana] 840 76050 0 97 ref|NP_567714.1|AMY1 (ALPHA-AMYLASE−LIKE); alpha- CS amylase [Arabidopsis thaliana] 841 13038 0 100 ref|NP_194382.1|fructose-bisphosphate aldolase, LN cytoplasmic [Arabidopsis thaliana] 842 13040 1.00E−104 92 gb|AAB66906.1|eukaryotic initiation factor (iso)-4F p28 LN subunit [Arabidopsis thaliana] 843 70716 1.00E−172 100 ref[NP_974170.1|serine/threonine protein kinase, putative HS [Arabidopsis thaliana] 843 76039 0 99 ref|NP_001078396.1|PPDK (PYRUVATE HS ORTHOPHOSPHATE DIKINASE) [Arabidopsis thaliana] 844 71611 0 99 ref|NP_001078396.1|PPDK (PYRUVATE CK PP ORTHOPHOSPHATE DIKINASE) [Arabidopsis thaliana] 845 70253 0 100 ref|NP_200694.1|CYP86A1 (cytochrome P450, family 86, HS CK subfamily A, polypeptide 1); oxygen binding [Arabidopsis thaliana] 846 14415 0 96 ref|NP_568054.1|SEC14 cytosolic factor, putative/ LN phosphoglyceride transfer protein, putative [Arabidopsis thaliana] 847 13718 4.00E−56 100 ref|NP_196413.1|unknown protein [Arabidopsis thaliana] LN sp|Q9SD88|U139 ARATH UPF0139 protein At5g07960 848 10706 0 88 gb|AAA19118.1|glutamyl-tRNA reductase CK HS 848 10709 0 88 gb|AAA19118.1|glutamyl-tRNA reductase LN 849 14340 1.00E−125 93 ref|NP_175332.1|unknown protein [Arabidopsis thaliana] LN 850 13471 1.00E−136 95 ref|NP_565858.1|unknown protein [Arabidopsis thaliana] LN 851 18304 1.00E−133 94 ref|NP_189283.1|TIP2 (TONOPLAST INTRINSIC HS PROTEIN 2); water channel [Arabidopsis thaliana] 852 13623 0 96 ref|NP_176001.2|GTP-binding protein-related [Arabidopsis DS thaliana] 853 18302 0 100 ref|NP_194702.2|NFC5 (NUCLEOSOME/CHROMATIN HS ASSEMBLY FACTOR GROUP C 5) [Arabidopsis thaliana] sp|Q9SU78|MSI5_ARATH WD-40 repeat-containing protein MSI5 854 15053 0 97 ref|NP_001031261.1|unknown protein [Arabidopsis LN thaliana] 855 15624 0 93 ref|NP_171975.2|RabGAP/TBC domain-containing protein LL PP [Arabidopsis thaliana] 856 70412 0 81 ref[NP_179257.1|nodulin family protein [Arabidopsis HS thaliana] 857 17902 0 91 ref|NP_564843.1|integral membrane transporter family PP protein [Arabidopsis thaliana] 858 14272 0 90 ref|NP_566584.1|YSL5 (YELLOW STRIPE LIKE 5); LN oligopeptide transporter [Arabidopsis thaliana] 859 15122 0 95 ref|NP_565817.2|glycogenin glucosyltransferase LN (glycogenin)-related [Arabidopsis thaliana] 859 70723 0 95 ref|NP_565817.2|glycogenin glucosyltransferase HS (glycogenin)-related [Arabidopsis thaliana] 860 14248 1.00E−154 79 ref|NP_176081.1|unknown protein [Arabidopsis thaliana] DS 861 13965 0 100 ref[NP_173104.1 |Per1-like family protein [Arabidopsis CK thaliana] 862 75912 1.00E−169 100 ref|NP_199075.1|unknown protein [Arabidopsis thaliana] CS LL 863 14344 1.00E−81 100 ref|NP_566785.1|universal stress protein (USP) family CS protein [Arabidopsis thaliana] 864 14807 0 89 gb|AAD20391.1|hypothetical protein [Arabidopsis thaliana] CS 865 17307 0 89 dbj|BAE98505.1|hypothetical protein [Arabidopsis thaliana] PP 866 16431 0 73 ref|NP_201248.1|octicosapeptide/Phox/Bem1p (PB1) LN domain-containing protein [Arabidopsis thaliana] 867 73075 0 96 ref|NP_187459.2|protein binding/zinc ion binding CS [Arabidopsis thaliana] 868 16323 9.00E−57 89 ref|NP_171768.2|transcription initiation factor IID (TFIID) LN 18 kDa subunit (TAFII-18) family protein [Arabidopsis thaliana] 869 14833 1.00E−141 90 ref|NP_176342.1|CCR4-NOT transcription complex SP protein, putative [Arabidopsis thaliana] 870 17030 0 95 gb|EAAG28899.1|AC008113_15F12A21.29 [Arabidopsis LL thaliana] 871 76414 0 99 ref|NP_180595.1|CIPK11 (SNF1-RELATED PROTEIN PEG KINASE 3.22, SOS3-INTERACTING PROTEIN 4); kinase [Arabidopsis thaliana] 872 16021 0 82 ref|NP_201301.1|CDKC;2 (CYCLIN-DEPENDENT KINASE LN C;2); kinase [Arabidopsis thaliana] 873 78701 0 93 ref|NP_564203.1|F-box family protein [Arabidopsis HS thaliana] 874 78702 0 93 ref|NP_565142.1|F-box family protein (FBX3) [Arabidopsis PEG thaliana] 875 15220 0 89 ref|NP_173623.1|kelch repeat-containing F-box family LN protein [Arabidopsis thaliana] sp|Q9LM55|FBK8_ARATH F-box/Kelch-repeat protein 876 15623 0 88 ref|NP_179623.1|transducin family protein/WD-40 repeat HS family protein [Arabidopsis thaliana] 877 19402 0 96 ref|NP_568408.1|F-box family protein/WD-40 repeat PP family protein [Arabidopsis thaliana] 878 70559 0 98 ref|NP_181061.1|SUVH5 (SU(VAR)3-9 HOMOLOG 5) LN [Arabidopsis thaliana] 879 15111 0 90 ref|NP_197821.1|ATXR6 (Arabidopsis thaliana Trithorax- DS related protein 6); DNA binding sp|Q9FNE9|ATXR6_ARATH Histone-lysine N- methyltransferase ATXR6 (Trithorax-related protein 6) (TRX-related protein 6) 880 70832 0 100 ref|NP_172633.1|CYP51G1 (CYTOCHROME P450 51); HS oxygen binding [Arabidopsis thaliana] 881 15129 4.00E−82 77 ref|NP_188372.1 |PHD finger family protein [Arabidopsis LN thaliana] 882 76086 0 91 ref|NP_192814.1|EMB1706 (EMBRYO DEFECTIVE 1706); PP S-adenosylmethionine-dependent methyltransferase [Arabidopsis thaliana] 883 15203 1.00E−158 94 gb|AAD30650.1|AC006085_23Similar to human CGI-33 CK protein [Arabidopsis thaliana] 884 70216 0 95 ref|NP_567665.2|CYP706A1 (cytochrome P450, family HS PP 706, subfamily A, polypeptide 1); oxygen binding [Arabidopsis thaliana] 885 14910 0 100 ref|NP_201191.1|UVR8 (UVB-RESISTANCE 8) DS [Arabidopsis thaliana] 886 70318 0 92 ref|NP_172325.2|ATCPNIFS/ATNFS2/ATSUFS/CPNIFS/ HS SUFS (CHLOROPLASTIC NIFS-LIKE CYSTEINE DESULFURASE); cysteine desulfurase/selenocysteine lyase/transaminase [Arabidopsis thaliana] 887 15207 1.00E−44 99 gb|AAG51737.1|AC068667_16beta-1,3 glucanase, SP putative; 26636-27432 [Arabidopsis thaliana] 888 14915 0 97 ref|NP_199393.1|CIPK19 (CIPK19); kinase [Arabidopsis LN thaliana] 889 15132 1.00E−152 80 ref|NP_187881.1|ZIP1 (ZINC TRANSPORTER 1 LN PRECURSOR); zinc ion transporter [Arabidopsis thaliana] 890 16229 0 100 gb|ABG54330.1|double HA-tagged mitogen activated SS protein kinase 3 [synthetic construct] 891 14932 0 100 ref|NP_568748.1|nucleotide-binding family protein DS [Arabidopsis thaliana] 892 76017 1.00E−180 100 ref|NP_568235.1|unknown protein [Arabidopsis thaliana] HS PP 893 15964 1.00E−44 100 ref|NP_566894.1|unknown protein [Arabidopsis thaliana] DS 894 17227 8.00E−83 73 gb|AAD03429.1|similar to nascent polypeptide associated CS complex alpha chain [Arabidopsis thaliana] 895 72952 0 96 ref|NP_564480.1|unknown protein [Arabidopsis thaliana] CS 896 73706 0 96 ref|NP_568221.1|protein kinase, putative [Arabidopsis HS SS thaliana] 897 18203 0 92 ref[NP_568919.1|APRR3 (PSEUDO-RESPONSE HS REGULATOR 3); transcription regulator [Arabidopsis thaliana] 898 16309 1.00E−163 88 ref|NP_195558.1|GGR (GERANYLGERANYL LN REDUCTASE); farnesyltranstransferase [Arabidopsis thaliana] 899 15986 3.00E−99 84 dbj|BAF02216.1|(hypothetical protein [Arabidopsis thaliana] DS 900 15987 2.00E−54 79 ref|NP_174170.1|glutaredoxin family protein [Arabidopsis DS thaliana] 901 16204 2.00E−59 100 ref|NP_566191.1|NADH-ubiquinone oxidoreductase- LN related [Arabidopsis thaliana] 902 11133 1.00E−114 100 ref|NP_563897.1|alanine racemase family protein LN [Arabidopsis thaliana] 903 73977 9.00E−67 100 ref|NP_194677.1|mitochondrial ATP synthase g subunit HS family protein [Arabidopsis thaliana] 904 15995 1.00E−176 84 ref|NP_564660.1|unknown protein [Arabidopsis thaliana] DS 904 18201 1.00E−176 84 ref|NP_564660.1|unknown protein [Arabidopsis thaliana] PP 905 16887 1.00E−164 100 ref|NP_171820.1|phenazine biosynthesis PhzC/PhzF PP family protein [Arabidopsis thaliana] 906 16213 1.00E−140 82 ref|NP_563991.1|unknown protein [Arabidopsis thaliana] HS 907 15507 0 96 ref|NP_172255.1|cupin family protein [Arabidopsis LN thaliana] 908 15508 3.00E−86 100 ref|NP_564937.1|unknown protein [Arabidopsis thaliana] LN 909 15959 3.00E−56 74 ref|NP_180097.1|unknown protein [Arabidopsis thaliana] LN 910 72427 0 93 ref|NP_568346.1|tubulin family protein [Arabidopsis HS thaliana] 911 19041 2.00E−85 82 ref|NP_565723.1|unknown protein [Arabidopsis thaliana] HS LN 912 17802 1.00E−118 100 ref|NP_187425.1|emp24/gp25L/p24 family protein HS [Arabidopsis thaliana] 913 19042 0 94 ref|NP_569048.1|ARA1 2; subtilase [Arabidopsis thaliana] HS 914 76053 0 94 ref|NP_172544.1|unknown protein [Arabidopsis thaliana] HS 915 16120 1.00E−56 90 ref|NP_192997.1|ribosomal protein CK L7Ae/L30e/S12e/Gadd45 family protein [Arabidopsis thaliana] 916 15424 1.00E−103 94 ref|NP_196647.1|CBS domain-containing protein HS [Arabidopsis thaliana] 917 16401 0 90 ref|NP_179995.1|CYP71B6 (CYTOCHROME P450 71B6); PP oxygen binding [Arabidopsis thaliana] 918 72417 0 100 gb|AAK25868.1|AF360158_1 unknown protein [Arabidopsis CK thaliana] 919 73702 0 90 ref|NP_564657.1|spliceosome protein-related [Arabidopsis HS SS thaliana] 920 70706 0 100 gb|AAD17366.1|similar to human phosphotyrosyl HS phosphatase activator PTPA (GB:X73478) [Arabidopsis thaliana] 921 71145 4.00E−57 86 gb|AAG40386.1|AF325034_1AT5g02160 [Arabidopsis HS thaliana] 922 11609 0 97 gb|AAC34228.1|putative cytochrome P450 [Arabidopsis LN thaliana] 923 71706 0 88 gb|AAF03464.1|AC009327_3 hypothetical protein CK [Arabidopsis thaliana] 924 17325 1.00E−144 86 ref|NP_563896.1|unknown protein [Arabidopsis thaliana] PP 925 70102 1.00E−166 100 ref|NP_353899.2|hypothetical protein Atu0877 HS [Agrobacterium tumefaciens str. C58] 926 70106 1.00E−151 92 ref|NP_353321.1|hypothetical protein Atu0291 HS [Agrobacterium tumefaciens str. C58] 927 70113 3.00E−94 94 ref|NP_013690.1|Adenine phosphoribosyltransferase, HS catalyzes the formation of AMP from adenine and 5- phosphoribosylpyrophosphate; involved in the salvage pathway of purine nucleotide biosynthesis; Apt1p [Saccharomyces cerevisiae] 928 70115 0 100 ref|NP_116623.1|Alanine:glyoxylate aminotransferase HS (AGT), catalyzes the synthesis of glycine from glyoxylate, which is one of three pathways for glycine biosynthesis in yeast; has similarity to mammalian and plant alanine:glyoxylate aminotransferases; Agx1p [Saccharomyces cerevisiae] 929 70118 0 94 ref|NP_012111.1|Mitochondrial glycerol-3-phosphate SP dehydrogenase; expression is repressed by both glucose and cAMP and derepressed by non-fermentable carbon sources in a Snf1p, Rsf1p, Hap2/3/4/5 complex dependent manner; Gut2p [Saccharomyces cerevisiae] 930 70128 9.00E−85 70 ref|NP_638658.1|membrane-bound proton-translocating HS pyrophosphatase [Xanthomonas campestris pv. campestris str. ATCC 33913] 931 70130 1.00E−161 99 ref|NP_639330.1|a-type carbonic anhydrase HS PEG [Xanthomonas campestris pv. campestris str. ATCC 33913] 932 17103 0 88 ref|NP_173155.1|CAT8 (CATIONIC AMINO ACID SS TRANSPORTER 8); cationic amino acid transporter [Arabidopsis thaliana] 933 72748 1.00E−33 74 ref|NP_568635.1|unknown protein [Arabidopsis thaliana] HS 934 17502 3.00E−94 74 ref|NP_565588.1|unknown protein [Arabidopsis thaliana] HS 935 17503 1.00E−130 100 ref[NP_176178.1[ATGSTU16 (Arabidopsis thaliana HS Glutathione S-transferase (class tau) 16); glutathione transferase 936 78708 1.00E−168 95 gb|AAK43902.1|AF370583_1 Unknown protein LL [Arabidopsis thaliana] 937 17504 1.00E−139 95 ref[NP_565634.1|harpin-induced protein-related/HIN1- HS LL PP related/harpin-responsive protein-related [Arabidopsis thaliana] 938 17132 1.00E−127 100 ref|NP_187978.1|seven in absentia (SINA) family protein LN [Arabidopsis thaliana] 939 72965 0 91 gb|AAN60250.1|unknown [Arabidopsis thaliana] LL 940 72796 3.00E−61 100 ref|NP_201508.1|RALFL34 (RALF-LIKE 34) [Arabidopsis CS thaliana] 941 16617 5.00E−96 100 ref|NP_355193.2|adenine phosphoribosyltransferase CS HS [Agrobacterium tumefaciens str. C58] 942 16640 0 100 ref|NP_355113.2|alcohol dehydrogenase [Agrobacterium HS tumefaciens str. C58] 943 16603 1.00E−132 85 ref[NP_357530.1|ribokinase [Agrobacterium tumefaciens HS str. C58] 944 16612 1.00E−137 100 ref|NP_010335.1|Triose phosphate isomerase, abundant LN SP glycolytic enzyme; mRNA half-life is regulated by iron availability; transcription is controlled by activators Reb1p, Gcr1p, and Rap1p through binding sites in the 5′ non- coding region; Tpi1p [Saccharomyces cerevisiae] 945 16614 1.00E−109 100 ref|NP_010741.1|Stress inducible cytoplasmic thioredoxin DS peroxidase; cooperates with Tsa1p in the removal of reactive oxygen, nitrogen and sulfur species using thioredoxin as hydrogen donor; deletion enhances the mutator phenotype of tsal mutants; Tsa2p [Saccharomyces cerevisiae] 946 78354 7.00E−80 100 ref|NP_192392.1|methionine sulfoxide reductase domain- SS containing protein/SeIR domain-containing protein [Arabidopsis thaliana] 947 17818 6.00E−19 60 ref|NP_564780.1|TIM13 (TIM13); protein translocase PP [Arabidopsis thaliana] 948 78370 3.00E−64 91 ref|NP_194900.1|TAFII15 (SALT TOLERANCE DURING HS GERMINATION 1); transcription factor [Arabidopsis thaliana] 949 70411 0 90 ref|NP_849806.1|UBP1A; mRNA3′-UTR binding SP [Arabidopsis thaliana] 950 19154 1.00E−151 89 ref|NP_197310.1|transcriptional factor B3 family protein HS LN PP [Arabidopsis thaliana] 951 19155 0 82 ref|NP_200906.2|nuclear transport factor 2 (NTF2) family HS protein/RNA recognition motif (RRM)-containing protein [Arabidopsis thaliana] 952 18307 0 94 ref|NP_194507.1|ACBP2 (ACYL-COA BINDING PROTEIN HS ACBP 2) [Arabidopsis thaliana] 953 72030 0 86 ref|NP_177367.1|zinc finger (C3HC4-type RING finger) LN family protein [Arabidopsis thaliana] 954 17916 1.00E−173 95 ref|NP_568839.1|CSN6A (COP9 signalosome subunit 6A) PP [Arabidopsis thaliana] 955 17917 0 96 ref|NP_188478.1|aspartyl protease family protein SS [Arabidopsis thaliana] 956 17334 0 94 ref|NP_178146.1|chloroplast ADP, ATP carrier protein 1/ PP ADP, ATP translocase 1/adenine nucleotide translocase 1 (AATP1) [Arabidopsis thaliana] 957 71531 0 100 ref|NP_565656.1|aldo/keto reductase family protein HS [Arabidopsis thaliana] 958 18441 7.00E−75 100 ref|NP_973779.1|lactoylglutathione lyase family protein/ HS glyoxalase I family protein [Arabidopsis thaliana] 959 19162 2.00E−73 85 ref|NP_563687.1|photosystem II family protein DS [Arabidopsis thaliana] 960 73205 0 98 ref|NP_190414.1|zinc finger (CCCH-type) family protein PEG [Arabidopsis thaliana] 961 18306 1.00E−172 100 ref|NP_566769.1|LAG1 (Longevity assurance gene 1) SS [Arabidopsis thaliana] 962 70808 0 97 ref|NP_196136.1|CESA3 (CELLULASE SYNTHASE 3); CS CK cellulose synthase/transferase, transferring glycosyl groups [Arabidopsis thaliana] 963 17653 1.00E−178 95 ref[NP_199155.1|zinc finger (C3HC4-type RING finger) LN family protein [Arabidopsis thaliana] 964 19535 0 81 ref|NP_567002.1|GCN5 (Histon acetyltransferase HAT1) HS [Arabidopsis thaliana] 965 71719 0 99 ref|NP_192044.1|DC1 domain-containing protein HS LL PP [Arabidopsis thaliana] 966 18546 1.00E−102 92 ref|NP_176285.1|AGL56 (AGAMOUS LIKE−56); DNA PP binding/transcription factor [Arabidopsis thaliana] 967 19534 0 78 ref|NP_566721.1|binding [Arabidopsis thaliana] HS 968 18421 0 96 gb|ABK06451.1|flag-tagged protein kinase domain of HS putative mitogen-activated protein kinase kinase kinase [synthetic construct] 969 18422 0 100 ref[NP_194498.1|MSP1 protein, putative/ HS intramitochondrial sorting protein, putative [Arabidopsis thaliana] 970 19539 0 95 ref|NP_191747.1|CYP78A9 (CYTOCHROME P450 78A9); HS PP oxygen binding [Arabidopsis thaliana] 971 19244 3.00E−74 88 ref|NP_565113.1|auxin-responsive family protein HS [Arabidopsis thaliana] 972 15803 1.00E−142 100 ref|NP_199675.2|cyclin family protein [Arabidopsis HS thaliana] 973 19545 0 100 ref|NP_568665.1|pentatricopeptide (PPR) repeat- HS containing protein [Arabidopsis thaliana] 974 10222 0 94 ref|NP_190896.1|CYP71B5 (CYTOCHROME P450 71B5); LN oxygen binding [Arabidopsis thaliana] 974 72356 0 94 ref|NP_190896.1|CYP71B5 (CYTOCHROME P450 71B5); CK PEG oxygen binding [Arabidopsis thaliana] 975 70425 0 98 ref|NP_200201.3|unknown protein [Arabidopsis thaliana] HS 976 19237 1.00E−150 95 ref|NP_199836.1|31 kDa ribonucleoprotein, chloroplast, HS putative/RNA-binding protein RNP-T, putative/RNA- binding protein 1/2/3, putative/RNA-binding protein cp31, putative [Arabidopsis thaliana] 977 71303 0 82 ref|NP_199431.1|KH domain-containing protein HS [Arabidopsis thaliana] 978 19240 1.00E−180 100 ref|NP_566576.1|meprin and TRAF homology domain- LN containing protein/MATH domain-containing protein [Arabidopsis thaliana] 979 18535 0 100 ref|NP_196179.1|oxidoreductase, 2OG-Fe(II) oxygenase HS family protein [Arabidopsis thaliana] 980 19450 0 94 ref|NP_565422.1|pentatricopeptide (PPR) repeat- LN containing protein [Arabidopsis thaliana] 981 18221 1.00E−66 100 ref|NP_193992.1|protease inhibitor/seed storage/lipid PP transfer protein (LTP) family protein [Arabidopsis thaliana] 982 18233 1.00E−110 87 ref|NP_193179.1|enoyl-CoA hydratase/isomerase family PP protein [Arabidopsis thaliana] 983 18236 1.00E−31 70 ref|NP_565410.1|unknown protein [Arabidopsis thaliana] PP 984 18238 1.00E−129 88 ref|NP_197105.1|3-oxo-5-alpha-steroid 4-dehydrogenase HS family protein/steroid 5-alpha-reductase family protein [Arabidopsis thaliana] 985 18309 1.00E−128 93 gb|AAM61596.1|DNA-binding protein [Arabidopsis CS PEG thaliana] 986 70337 0 85 gb|AAP84710.2|metacaspase 7 [Arabidopsis thaliana] HS 987 18319 1.00E−105 89 ref|NP_172721.1|DDF1 (DWARF AND DELAYED LN FLOWERING 1); DNA binding/transcription factor [Arabidopsis thaliana] 988 70338 1.00E−172 85 ref NP_200445.1|zinc finger (C3HC4-type RING finger) LL family protein [Arabidopsis thaliana] 989 10471 1.00E−114 84 dbj|BAF00210.1|hypothetical protein [Arabidopsis thaliana] DS 990 18331 1.00E−114 63 ref|NP_565124.1|nucleic acid binding [Arabidopsis thaliana] CS 991 10228 0 97 ref|NP_563880.1|TIF3H1 (eukaryotic translation initiation LN factor 3 subunit H1); translation initiation factor [Arabidopsis thaliana] 991 10473 0 97 ref|NP_563880.1|TIF3H1 (eukaryotic translation initiation LN factor 3 subunit H1); translation initiation factor [Arabidopsis thaliana] 992 18261 1.00E−167 91 ref|NP_563732.1|peroxidase, putative [Arabidopsis PP thaliana] 993 18848 0 94 ref[NP_177805.1|O-methyltransferase family 2 protein LN [Arabidopsis thaliana] 994 18268 1.00E−130 92 gb|AAM62813.1|unknown [Arabidopsis thaliana] PP 995 18345 0 92 ref|NP_182320.1|SWA1 (SLOW WALKER1); nucleotide binding [Arabidopsis thaliana] 996 73607 0 92 ref|NP_851068.1|WD-40 repeat family protein [Arabidopsis HS thaliana] 997 18352 1.00E−166 ref|NP_201275.1|nodulin MtN21 family protein HS SS PEG 83 [Arabidopsis thaliana] 998 18357 1.00E−171 100 ref|NP_172866.1|mitochondrial substrate carrier family PP protein [Arabidopsis thaliana] 999 19423 0 100 ref|NP_177020.1|CUT1 (CUTICULAR 1); acyltransferase DS [Arabidopsis thaliana] 1000 78373 0 94 ref|NP_179537.1|CKL5 (Casein Kinase I-like 5); casein CK HS kinase 1/kinase [Arabidopsis thaliana] 1001 70603 0 100 ref|NP_175081.1|ALDH3H1 (ALDEHYDE HS LN DEHYDROGENASE 4); 3-chloroallyl aldehyde dehydrogenase/aldehyde dehydrogenase (NAD) [Arabidopsis thaliana] 1002 19616 1.00E−159 100 ref|NP_563789.1|SMO2-2 (sterol 4-alpha-methyl-oxidase HS 2); C-4 methylsterol oxidase [Arabidopsis thaliana] 1003 19425 1.00E−164 91 ref|NP_564407.1|electron carrier/iron ion binding DS [Arabidopsis thaliana] 1004 19426 1.00E−152 89 ref|NP_564428.1|unknown protein [Arabidopsis thaliana] PP 1005 18382 2.00E−51 87 refNP_564651.1|unknown protein [Arabidopsis thaliana] PP 1006 71536 4.00E−86 86 ref|NP_564747.1|ZCF37 [Arabidopsis thaliana] HS 1007 70419 6.00E−88 66 ref|NP_564888.1|unknown protein [Arabidopsis thaliana] LL CK DS 1008 70827 6.00E−85 100 ref|NP_189667.1|zinc finger (C3HC4-type RING finger) HS family protein [Arabidopsis thaliana] 1009 19311 0 94 ref|NP_010849.1|Ferrioxamine B transporter, member of LN the ARN family of transporters that specifically recognize siderophore-iron chelates; transcription is induced during iron deprivation and diauxic shift; potentially phosphorylated by Cdc28p; Sit1p [Saccharomyces cerevisiae] 1010 19323 0 92 ref|NP_354642.2|malic enzyme LL [Agrobacterium tumefaciens str. C58] 1011 19320 0 100 ref|NP_0l2542.1|Glyceraldehyde-3-phosphate HS dehydrogenase, isozyme 2, involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate; detected in the cytoplasm and cell-wall; Tdh2p [Saccharomyces cerevisiae] 1012 73613 0 95 ref|NP_197104.1|NIK1 (NSP-INTERACTING KINASE 1); CK kinase [Arabidopsis thaliana] 1013 70432 1.00E−162 91 ref|NP_196709.1|GTP binding [Arabidopsis thaliana] SS 1014 70433 0 100 ref|NP_196957.1|transducin family protein/WD-40 repeat HS family protein [Arabidopsis thaliana] 1015 70434 1.00E−142 94 ref|NP_180497.1|tropinone reductase, putative/tropine HS dehydrogenase, putative [Arabidopsis thaliana] 1016 72614 1.00E−128 79 ref|NP_197757.1|sterile alpha motif (SAM) domain- LL containing protein [Arabidopsis thaliana] 1017 70436 7.00E−35 70 ref|NP_197966.1|early nodulin-related [Arabidopsis CS HS thaliana] 1018 74226 0 92 dbj|BAB02016.1|MAP kinase [Arabidopsis thaliana] PP 1019 70439 1.00E−123 91 ref|NP_191247.1|VQ motif-containing protein [Arabidopsis HS PEG thaliana] 1020 70446 1.00E−128 100 ref|NP_568972.2|unknown protein [Arabidopsis thaliana] CS 1021 70613 0 93 ref|NP_174145.1|unknown protein [Arabidopsis thaliana] PEG 1022 70447 0 97 refNP_175977.1|uracil phosphoribosyltransferase, CK putative/UMP pyrophosphorylase, putative/UPRTase, putative [Arabidopsis thaliana] ref|NP_974037.1| uracil phosphoribosyltransferase, putative/UMP pyrophosphorylase, putative/UPRTase, putative [Arabidopsis thaliana] 1023 71725 0 67 gb|ABE65946.1|nucleolin [Arabidopsis thaliana] CK 1024 70462 9.00E−73 92 ref|NP_567037.1|ARR17 (response regulator 17); PEG transcription regulator/two-component response regulator [Arabidopsis thaliana] 1025 70545 0 95 ref]NP_176108.3|bZIP family transcription factor, SP [Arabidopsis thaliana] 1026 70741 0 100 gb|AAM78097.1|AT4g18060/F15J5_30 [Arabidopsis HS thaliana] 1027 19702 0 97 ref|NP_011904.1|Protein of unknown function, green HS fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; msc7 mutants are defective in directing meiotic recombination events to homologous chromatids; Msc7p [Saccharomyces cerevisiae] 1028 19985 1.00E−140 86 gb|AAA88792.1|nucleosome assembly protein 1 HS 1029 19775 1.00E−80 54 refNP_175779.1|unknown protein [Arabidopsis thaliana] CK HS PP LN 1030 19829 3.00E−56 42 ref|NP_565892.1|unknown protein [Arabidopsis thaliana] CS 1031 19982 1.00E−123 79 gb|AAV49506.1|L-galactose-1-phosphate phosphatase HS PEG [Actinidia deliciosa] 1032 19755 1.00E−110 63 emb|CA023381.1|unnamed protein product [Vitis vinifera] HS 1033 19732 0 96 dbj|BAA22559.1|squalene synthase [Glycine max] PP 1034 70365 0 91 gb|AAQ84169.1|1-deoxy-D-xylulose 5-phosphate synthase CS [Pueraria montana var. lobata] 1035 10476 1.00E−168 86 ref|NP_194096.1|CDPK6 (CALCIUM-DEPENDENT LN PROTEIN KINASE 6); anion channel/calcium-and calmodulin-dependent protein kinase/kinase [Arabidopsis thaliana] 1036 19987 0 83 emb|CAO67062.1|unnamed protein product [Vitis vinifera] HS 1037 19893 1.00E−166 85 gb|ABC75353.2|Intracellular chloride channel HS [Medicago truncatula] 1038 19983 6.00E−92 60 emb|CA039739.1|unnamed protein product [Vitis vinifera] HS LL 1039 19825 1.00E−40 39 emb|CA018125.1|unnamed protein product [Vitis vinifera] HS 1040 19919 1.00E−121 77 emb|CA061472.1|unnamed protein product [Vitis vinifera] HS 1041 19979 0 67 emb[CA068238.1|unnamed protein product [Vitis vinifera] HS 1042 19786 2.00E−80 75 emb|CA048404.1|unnamed protein product [Vitis vinifera] HS LN 1043 70903 0 76 emb|CA066035.1|unnamed protein product [Vitis vinifera] HS PP PEG 1044 70970 1.00E−102 67 ref|NP_200538.1|unknown protein [Arabidopsis thaliana] HS 1045 70980 0 89 dbj|BAE71243.1|putative galactose kinase [Trifolium pratense] CK 1046 70936 1.00E−158 49 emb|CA071465.1|unnamed protein product [Vitis vinifera] HS 1047 71425 1.00E−160 74 emb|CA014679.1|unnamed protein product [Vitis vinifera] DS 1048 78666 3.00E−45 83 ref|NP_192698.1|GASA3 (GAST1 PROTEIN HOMOLOG 3) LN [Arabidopsis thaliana] 1049 71202 1.00E−163 95 ref|NP_194179.1|serine/threonine protein kinase, putative LN [Arabidopsis thaliana] 1050 78973 0 90 ref[NP_565672.1|DRB2 (DSRNA-BINDING PROTEIN 2); LL double-stranded RNA binding [Arabidopsis thaliana] 1051 76411 1.00E−179 99 ref|NP_172864.1|2-oxoglutarate-dependent dioxygenase, PP putative [Arabidopsis thaliana] 1052 70635 4.00E−64 100 ref|NP_851278.1|senescence-associated family protein HS [Arabidopsis thaliana] 1053 73715 0 92 ref|NP_198428.1|G6PD1 (GLUCOSE-6-PHOSPHATE PEG DEHYDROGENASE 1); glucose-6-phosphate 1-dehydrogenase [Arabidopsis thaliana] 1054 70638 6.00E−79 89 ref|NP_197398.1|AWPM-19-like membrane family protein HS LN [Arabidopsis thaliana] 1055 70642 1.00E−176 92 ref|NP_191315.1|aspartate/glutamate/uridylate kinase HS family protein [Arabidopsis thaliana] 1056 70643 0 96 ref|NP_191703.1|ATCYSC1 (BETA-SUBSTITUTED ALA HS SYNTHASE 3;1); L-3-cyanoalanine synthase/cysteine synthase [Arabidopsis thaliana] 1057 71564 1.00E−121 95 emb|CAA47753.1|proteosome subunit [Arabidopsis HS SP thaliana] 1058 75039 1.00E−175 90 ref|NP_188659.1|mitochondrial substrate carrier family LN protein [Arabidopsis thaliana] 1059 70653 8.00E−82 100 ref|NP_566365.1|unknown protein [Arabidopsis thaliana] PEG 1060 70655 4.00E−87 82 ref|NP_566619.1|unknown protein [Arabidopsis thaliana] LL PEG 1061 78321 0 97 ref|NP_181404.1|MVD1 (mevalonate diphosphate DS HS decarboxylase 1) [Arabidopsis thaliana] 1062 78307 0 100 ref|NP_182079.1|CYP76C4 (cytochrome P450, family 76, CK subfamily C, polypeptide 4); oxygen binding [Arabidopsis thaliana] 1063 71808 0 91 ref|NP_182082.2|CYP76C3 (cytochrome P450, family 76, HS subfamily C, polypeptide 3); oxygen binding [Arabidopsis thaliana] 1064 71810 0 97 gb|AAF88087.1|AC025417_15T12C24.27 [Arabidopsis LN thaliana] 1065 71313 0 100 ref|NP_187667.1|CYP77A7 (cytochrome P450, family 77, CS subfamily A, polypeptide 7, unfertilized embryo sac 9); oxygen binding [Arabidopsis thaliana] 1066 72349 1.00E−134 100 ref|NP_191072.1ref|NP_566619.1 | TT5 (TRANSPARENT TESTA 5); SP chaicone isomerase [Arabidopsis thaliana] 1067 71318 0 90 ref|NP_189261.1|CYP71B34 (cytochrome P450, family 71, HS subfamily B, polypeptide 34); oxygen binding [Arabidopsis thaliana] 1068 71812 0 92 ref|NP_195705.1|CYP79B2 (cytochrome P450, family 79, LN subfamily B, polypeptide 2); oxygen binding [Arabidopsis thaliana] 1069 74060 0 90 ref|NP_188731.1|CYP705A32 (cytochrome P450, family DS 705, subfamily A, polypeptide 32); oxygen binding [Arabidopsis thaliana] 1070 71816 0 93 ref|NP_568025.1|CYP81F3 (cytochrome P450, family 81, LL subfamily F, polypeptide 3); oxygen binding [Arabidopsis thaliana] 1071 71569 1.00E−142 95 ref|NP_189364.1|ATPHB4 (PROHIBITIN 4) [Arabidopsis CS thaliana] 1072 70672 0 100 ref|NP_567641.1|PRXR1 (peroxidase 42); peroxidase PP [Arabidopsis thaliana] 1073 71336 0 96 ref[NP_563762.1|VHS domain-containing protein/GAT DS domain-containing protein [Arabidopsis thaliana] 1074 71337 1.00E−179 100 ref|NP_179721.1|mannose 6-phosphate reductase HS (NADPH-dependent), putative [Arabidopsis thaliana] 1075 71339 0 93 ref|NP_200747.1|XH/XS domain-containing protein CS [Arabidopsis thaliana] 1076 71825 0 87 ref|NP_195998.2|TRFL10 (TRF-LIKE 10); DNA binding LN [Arabidopsis thaliana] 1077 73696 1.00E−166 86 ref|NP_192864.1|MADS-box family protein [Arabidopsis SP thaliana] 1078 70682 1.00E−129 94 ref[NP_001078595.1|RNA recognition motif (RRM)- HS containing protein [Arabidopsis thaliana] 1079 70686 1.00E−117 75 ref|NP_199096.1|ATU2AF35B; RNA binding [Arabidopsis SP LL thaliana] 1080 78316 0 100 ref|NP_192085.1|DC1 domain-containing protein SS [Arabidopsis thaliana] 1081 71667 0 100 ref|NP_013976.1|Glutamate decarboxylase, converts DS glutamate into gamma-aminobutyric acid (GABA) during glutamate catabolism; involved in response to oxidative stress; Gadip [Saccharomyces cerevisiae] 1082 71695 0 77 emb|CAA75577.1|L-ascorbate oxidase CK [Medicago truncatula] 1083 71696 0 96 gb|AAB03258.1|phosphoinositide-specific phospholipase C HS LN P13 1084 72475 1.00E−111 83 gb|AAF21310.1|seed maturation protein PM24 HS [Glycine max] 1085 71677 1.00E−125 77 gb|ABD28522.1|Cupin, RmIC-type [Medicago truncatula] CK 1086 71691 7.00E−34 35 emb|CA044124.1|unnamed protein product [Vitis vinifera] CS 1087 72476 1.00E−122 70 emb|CA047395.1|unnamed protein product [Vitis vinifera] HS 1088 70803 0 97 ref|NP_850874.1|glutamate-tRNA ligase, putative/ SP LN glutamyl-tRNA synthetase, putatuve/GluRS, putative [Arabidopsis thaliana] 1089 71612 0 94 ref|NP_192179.1|SULTR3;2 (SULFATE TRANSPORTER LL 3;2); sulfate transporter [Arabidopsis thaliana] 1090 71637 0 88 gb|AAD52696.1|AF087819_1 auxin transport protein LN [Arabidopsis thaliana] 1091 71629 0 97 ref|NP_565924.1|unknown protein [Arabidopsis thaliana] HS PEG 1092 71622 0 97 ref|NP_566085.1|APRR9 (PSEUDO-RESPONSE REGULATOR 9); transcription regulator [Arabidopsis LN thaliana] 1093 70810 0 91 ref|NP_175610.1|mitochondrial processing peptidase alpha HS SS subunit, putative [Arabidopsis thaliana] 1094 72452 6.00E−76 77 ref|NP_199889.1|auxin-responsive family protein LN [Arabidopsis thaliana] 1095 74071 0 93 ref|NP_174516.1|ribose-phosphate pyrophosphokinase 2/ phosphoribosyl diphosphate synthetase 2 (PRS2) LL [Arabidopsis thaliana] 1096 11042 2.00E−89 93 ref|NP_179709.1|peptidyl-prolyl cis-trans isomerase/ LN cyclophilin (CYP2)/rotamase [Arabidopsis thaliana] 1097 72510 0 89 ref|NP_196865.1|unknown protein [Arabidopsis thaliana] CK 1098 72537 1.00E−124 82 ref|NP_851118.1|unknown protein [Arabidopsis thaliana] HS LN 1099 72541 9.00E−57 88 ref|NP_568684.1|unknown protein [Arabidopsis thaliana] PP 1100 72617 4.00E−88 100 ref|NP_568761.1|unknown protein [Arabidopsis thaliana] LL 1101 73755 1.00E−132 100 ref|NP_200501_(;)1|cysteine protease inhibitor [Arabidopsis PP SS thaliana] 1102 72630 2.00E−86 93 ref|NP_201267.1|C/VIF2 (CELL WALL/VACUOLAR SP INHIBITOR OF FRUCTOSIDASE 2); pectinesterase inhibitor [Arabidopsis thaliana] 1103 72645 5.00E−37 75 ref|NP_180615.1|photosystem II reaction centerW (PsbW) LN protein-related [Arabidopsis thaliana] 1104 72647 5.00E−43 100 ref|NP_566036.1|protease inhibitor/seed storage/lipid LN transfer protein (LTP) family protein [Arabidopsis thaliana] 1105 14316 1.00E−55 86 ref|NP_188703.1| histone H2A, putative [Arabidopsis DS thaliana] 1106 73689 6.00E−79 100 ref|NP_173037.1|transducin family protein/WD-40 repeat DS SS family protein [Arabidopsis thaliana] 1107 73345 0 92 ref|NP_174226.1|transducin family protein/WD-40 repeat HS LN family protein [Arabidopsis thaliana] 1108 73347 0 100 ref|NP_177513.2|transducin family protein/WD-40 repeat SP family protein [Arabidopsis thaliana] 1109 73231 0 84 ref|NP_196332.1|leucine-rich repeat family protein PP [Arabidopsis thaliana] 1110 78325 0 84 ref|NP_171637.1|aspartyl protease family protein HS [Arabidopsis thaliana] 1111 72658 1.00E−138 93 ref|NP_172224.1|tropinone reductase, putative/tropine PEG dehydrogenase, putative [Arabidopsis thaliana] 1112 72660 3.00E−78 82 ref|NP_564585.1|zinc finger (AN1-like) family protein LN [Arabidopsis thaliana] 1113 72662 5.00E−49 100 ref|NP_179096.1|gibberellin-regulated family protein LN [Arabidopsis thaliana] 1114 73352 0 97 ref|NP_566304.1|armadillo/beta-catenin repeat family LN protein/U-box domain-containing protein [Arabidopsis thaliana] 1115 72814 0 100 ref|NP_566558.1|F-box family protein [Arabidopsis PP CS PEG thaliana] 1116 72816 0 100 ref|NP_566824.1|CARA (CARBAMOYL PHOSPHATE PP SYNTHETASE A); carbamoyl-phosphate synthase (glutamine-hydrolyzing) [Arabidopsis thaliana] 1117 72820 0 89 ref|NP_194653.1|leucine-rich repeat family protein/ LL extensin family protein [Arabidopsis thaliana] 1118 73353 0 97 ref|NP_194713.1|MTO2 (METHIONINE OVER- HS PEG ACCUMULATOR); threonine synthase [Arabidopsis thaliana] 1119 75066 1.00E−134 91 ref|NP_175644.1|ABA2 (ABA DEFICIENT 2); PEG oxidoreductase [Arabidopsis thaliana] 1120 78337 2.00E−40 78 dbj|BAD43663.1|unknown protein [Arabidopsis thaliana] PEG 1121 73317 0 96 ref|NP_200121.4|oxidoreductase [Arabidopsis thaliana] LN 1122 73318 0 94 ref|NP_568145.1|short-chain dehydrogenase/reductase CS (SDR) family protein [Arabidopsis thaliana] 1123 73749 0 97 gb|AAG51266.1|AC027135_7protein kinase, putative CS [Arabidopsis thaliana] 1124 18704 0 88 ref|NP_201234.1|DCT/DIT2.1 (DICARBOXYLATE PEG TRANSPORT); oxoglutarate:malate antiporter [Arabidopsis thaliana] 1125 73221 1.00E−162 82 ref[NP_563785.1|C2 domain-containing protein CK LL [Arabidopsis thaliana] 1126 71125 1.00E−117 97 ref|NP_172671.1|Rho-GDP-dissociation inhibitor family protein [Arabidopsis thaliana] 1127 76203 0 97 ref|NP_200678.2|phosphoinositide-specific phospholipase PEG C family protein [Arabidopsis thaliana] 1128 75067 0 100 ref|NP_566565.1|peroxidase, putative [Arabidopsis PEG thaliana] 1129 73729 0 100 ref|NP_194944.1|CYP96A2 (cytochrome P450, family 96, LL subfamily A, polypeptide 2); oxygen binding [Arabidopsis thaliana] 1130 75206 0 95 ref|NP_197962.1|GA3 (GA REQUIRING 3); oxygen HS binding [Arabidopsis thaliana] 1131 73248 0 100 ref|NP_200532.1|CYP81F2 (cytochrome P450, family 81, HS subfamily F, polypeptide 2); oxygen binding [Arabidopsis thaliana] 1132 73738 0 93 ref|NP_198641.1|serine/threonine protein kinase, putative DS [Arabidopsis thaliana] 1133 73332 0 97 ref|NP_173685.1|SUC2 (SUCROSE−PROTON PP SYMPORTER 2); carbohydrate transporter/ sucrose; hydrogen symporter/sugar porter [Arabidopsis thaliana] 1134 78335 0 100 ref|NP_189582.1|UDP-glucose 6-dehydrogenase, putative HS LL PP [Arabidopsis thaliana] 1135 75821 6.00E−76 90 ref|NP_190424.1|unknown protein [Arabidopsis thaliana] LL 1136 72038 0 97 emb|CAA1 8501.1|Calcium-dependent serine/threonine HS protein kinase [Arabidopsis thaliana] 1137 72027 0 91 ref|NP_849857.1|copine-related [Arabidopsis thaliana] DS 1138 72016 0 97 ref|NP_200887.1|ATGCN1 [Arabidopsis thaliana general CS control non-repressible 1) 1139 70835 1.00E−128 82 ref|NP_181461.1|PGPS1 SS (PHOSPHATIDYLGLYCEROLPHOSPHATE + SYNTHASE + 1); CDP-alcohol phosphatidyltransferase [Arabidopsis thaliana] 1140 72044 0 99 ref|NP_014446.1|Protein proposed to interact with CS phospholipid translocases, shares similarity to Cdc50p; Ynr048wp [Saccharomyces cerevisiae] 1141 72092 0 92 ref|NP_010796.1|High-affinity glutamine permease, also CK transports Leu, Ser, Thr, Cys, Met and Asn; expression is fully dependent on Grrip and modulated by the Ssy1p- Ptr3p-Ssy5p (SPS) sensor of extracellular amino acids; Gnp1p [Saccharomyces cerevisiae] 1142 72124 1.00E−173 55 emb|CA064952.1|unnamed protein product [Vitis vinifera] HS 1143 72110 1.00E−172 63 emb|CAN75218.1|hypothetical protein [Vitis vinifera] HS 1144 73916 1.00E−162 57 ref|NP_569047.1|SKIP2 (SKP1 INTERACTING PARTNER 2); HS ubiquitin-protein ligase [Arabidopsis thaliana] 1145 74268 0 100 ref|NP_186851.1|aspartate kinase, lysine-sensitive, HS LL putative [Arabidopsis thaliana] 1146 74269 0 94 ref|NP_566764.1|bile acid:sodium symporter family protein DS [Arabidopsis thaliana] 1147 77902 0 96 ref]NP_197021.2|tyrosyl-DNA phosphodiesterase-related SS [Arabidopsis thaliana] 1148 74273 1.00E−180 100 ref|NP_199285.1|molybdenum cofactor sulfurase family HS protein [Arabidopsis thaliana] 1149 74280 1.00E−165 94 emb|CAA58893.1|cysteine synthase [Arabidopsis thaliana] HS 1150 74281 0 94 ref|NP_197655.1|prephenate dehydratase family protein LL [Arabidopsis thaliana] 1151 74287 0 100 ref[NP_974217.1|SUVR4 [Arabidopsis thaliana] CK HS 1152 73767 1.00E−156 100 ref|NP_194231.1|nodulin MtN3 family protein [Arabidopsis LN thaliana] 1153 77304 0 100 ref|NP_175700.2|catalytic [Arabidopsis thaliana] CK HS PEG 1154 73761 0 95 ref|NP_566683.1|mitochondrial substrate carrier family LL protein [Arabidopsis thaliana] 1155 74721 0 93 ref|NP_194568.1|AAC3 (ADP/ATP CARRIER 3); ATPADP LL antiporter/binding [Arabidopsis thaliana] 1156 74719 0 91 ref|NP_198474.1|protein phosphatase 2C, putative/PP2C, CK putative [Arabidopsis thaliana] 1157 74257 0 98 ref|NP_179113.2|fatty acid elongase, putative [Arabidopsis DS HS thaliana] 1158 72749 0 95 ref|NP_176767.1|regulator of chromosome condensation HS LL (RCC1) family protein/zinc finger protein-related [Arabidopsis thaliana] 1159 72703 2.00E−77 92 ref|NP_013963.1|Subunit (17 kDa) of TFIID and SAGA PEG complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3; Taf9p [Saccharomyces cerevisiae] 1160 72763 0 98 ref|NP_009691.1|Protein arginine N-methyltransferase that SS exhibits septin and Hsl1p-dependent bud neck localization and periodic Hsl1p-dependent phosphorylation; required along with Hsl1p for bud neck recruitment, phosphorylation, and degradation of Swe1p; Hsl7p [Saccharomyces cerevisiae] 1161 72775 1.00E−172 100 ref|NP_009718.1|Catalytic subunit of the main cell cycle HS cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates; Cdc28p [Saccharomyces cerevisiae] 1162 72728 0 96 ref|NP_013106.1|Cytoplasmic response regulator, part of a CS two-component signal transducer that mediates osmosensing via a phosphorelay mechanism; dephosphorylated form is degraded by the ubiquitin- proteasome system; potential Cdc28p substrate; Ssk1p [Saccharomyces cerevisiae] 1163 72776 1.00E−101 92 gb|EDN62754.1|oxidant-induced cell cycle arrest HS [Saccharomyces cerevisiae YJM789] 1164 72717 1.00E−131 100 ref|NP_011075.1|TATA-binding protein, general DS transcription factor that interacts with other factors to form the preinitiation complex at promoters, essential for viability; Spt15p [Saccharomyces cerevisiae] 1165 72718 1.00E−159 90 ref|NP_011400.1|Activating gamma subunit of the AMP- DS activated Snflp kinase complex (contains Snflp and a Sip1p/Sip2p/Gal83p family member); activates glucose- repressed genes, represses glucose-induced genes; role in sporulation, and peroxisome biogenesis; Snf4p [Saccharomyces cerevisiae] 1166 11715 0 93 ref|NP_187616.1|OMR1 (L-O-METHYLTHREONINE LN RESISTANT 1); threonine ammonia-lyase [Arabidopsis thaliana] 1167 72779 0 93 ref|NP_011622.1|B-type cyclin involved in cell cycle DS progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome; Clb1p [Saccharomyces cerevisiae] 1168 72791 0 100 ref|NP_009709.1|Protein of unknown function, required for DS HS normal localization of actin patches and for normal tolerance of sodium ions and hydrogen peroxide; localizes to both cytoplasm and nucleus; Apd1p [Saccharomyces cerevisiae] 1169 72732 0 100 ref|NP_013662.1|Putative protein of unknown function; HS non-essential gene; null mutant displays increased frequency of mitochondrial genome loss (petite formation); Aim32p [Saccharomyces cerevisiae] 1170 73027 1.00E−125 93 ref|NP_187445.1|Rho GDP-dissociation inhibitor family CS protein [Arabidopsis thaliana] 1171 73058 0 96 ref|NP_175591.1|leucine-rich repeat protein kinase, CK putative [Arabidopsis thaliana] 1172 73126 0 95 ref|NP_173076.1|protein kinase family protein [Arabidopsis PEG thaliana] 1173 73138 0 91 ref|NP_356682.2|aldehyde dehydrogenase [Agrobacterium HS tumefaciens str. C58] 1174 73174 0 94 ref|NP_241069.1|glycine betaine aldehyde dehydrogenase HS [Bacillus halodurans C-125] 1175 73186 0 99 ref|NP_241405.1|NADP-dependent aldehyde HS LN dehydrogenase [Bacillus halodurans C-125] 1176 11141 0 100 ref|NP_568064.1|AGT2 (ALANINE:GLYOXYLATE LN AMINOTRANSFERASE 2); alanine-glyoxylate) transaminase [Arabidopsis thaliana] 1177 73139 0 89 ref[NP_242876.1|aldehyde dehydrogenase [Bacillus CS halodurans C-125] 1178 73128 0 97 ref|NP_388272.1|4-aminobutyrate aminotransferase HS [Bacillus subtilis subsp. subtilis str. 168] 1179 73164 0 93 ref[NP_389241.1|transaminase [Bacillus subtilis subsp. PEG subtilis str. 168] 1180 73117 0 97 ref|NP_391762.1|aldehyde dehydrogenase [Bacillus CS HS subtilis subsp. subtilis str. 168] 1181 73142 0 99 ref|YP_585121.1|glyceraldehyde-3-phosphate PP SS dehydrogenase, type I [Ralstonia metallidurans CH34] 1182 73990 1.00E−154 90 ref|NP_949547.1|glutaminase [Rhodopseudomonas HS palustris CGA009] 1183 73166 1.00E−117 100 ref|NP_384268.1|phosphoglyceromutase [Sinorhizobium SS meliloti 1021] 1184 73178 0 91 ref|NP_385430.1|PUTATIVE AMINOTRANSFERASE LL PROTEIN [Sinorhizobium meliloti 1021] 1185 73190 1.00E−142 99 ref|NP_385544.1|PROBABLE TRIOSEPHOSPHATE PEG ISOMERASE PROTEIN [Sinorhizobium meliloti 1021] 1186 73131 0 99 ref|NP_386510.1|beta amino acid-pyruvate transaminase CK [Sinorhizobium meliloti 1021] 1187 73108 0 92 ref|NP_929378.1|pyruvate kinase [Photorhabdus CK luminescens subsp. laumondii TTO1] 1188 73074 1.00E−171 87 gb|AAO17215.1|Epd [Photorhabdus luminescens] HS 1189 73132 1.00E−80 100 ref|NP_390154.1|nucleoside diphosphate kinase [Bacillus CS subtilis subsp. subtilis str. 168] 1190 73146 2.00E−94 93 ref|NP_931715.1|inorganic pyrophosphatase DS [Photorhabdus luminescens subsp. laumondii TTO1] 1191 73147 0 97 ref|NP_015444.1|B-type cyclin involved in cell cycle HS progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome; Clb2p [Saccharomyces cerevisiae] 1192 73080 0 92 gb|AAB17351.1|protein phosphatase type 2C LN [Saccharomyces cerevisiae] 1193 73077 0 97 ref|NP_010018.1|Endosomal protein that regulates cell HS polarity, controls polarized growth; similar to Ynr048wp and Lem3p; Cdc50p [Saccharomyces cerevisiae] 1194 73183 0 93 ref[NP_011895.1|Serine/threonine MAP kinase involved in CS HS regulating the maintenance of cell Wall integrity and progression through the cell cycle; regulated by the PKC1- mediated signaling pathway; Slt2p [Saccharomyces cerevisiae] 1195 73018 0 ref|NP_014582.1|NAD-dependent glycerol 3-phosphate HS 100 dehydrogenase, homolog of Gpd1p, expression is controlled by an oxygen-independent signaling pathway required to regulate metabolism under anoxic conditions; located in cytosol and mitochondria; Gpd2p [Saccharomyces cerevisiae] 1196 73112 0 97 ref|NP_014271.1|Homolog of human tumor suppressor HS gene PTEN/MMAC1/TEP1 that has lipid phosphatase activity and is linked to the phosphatidylinositol signaling pathway; plays a role in normal sporulation; Tep1p [Saccharomyces cerevisiae] 1197 73988 0 83 ref|NP_013664.1|ER localized integral membrane protein SS PEG that may promote secretion of certain hexose transporters, including Gal2p; involved in glucose-dependent repression; Gsf2p [Saccharomyces cerevisiae] 1198 10908 2.00E−61 100 ref|NP_199112.1|ATTRX3 (thioredoxin H-type 3); thiol- CK disulfide exchange intermediate [Arabidopsis thaliana] 1198 11147 2.00E−61 100 ref|NP_199112.1|ATTRX3 (thioredoxin H-type 3); thiol- LN disulfide exchange intermediate [Arabidopsis thaliana] 1199 72909 0 95 ref|NP_011569.1|High affinity methionine permease, HS integral membrane protein with 13 putative membrane- spanning regions; also involved in cysteine uptake; Mup1p [Saccharomyces cerevisiae] 1200 73987 0 94 ref|NP_010444.1|Component of the SPS plasma PP SS membrane amino acid sensor system (Ssy1p-Ptr3p- Ssy5p), which senses external amino acid concentration and transmits intracellular signals that result in regulation of expression of amino acid permease genes; Ssy1p [Saccharomyces cerevisiae] 1201 72922 0 91 ref|NP_010082.1|Putative transporter, member of the LL sugar porter family; Ydl199cp [Saccharomyces cerevisiae] 1202 73036 0 95 ref|NP_010022.1|Plasma membrane permease, mediates CS HS uptake of glycerophosphoinositol and glycerophosphocholine as sources of the nutrients inositol and phosphate; expression and transport rate are regulated by phosphate and inositol availability; Git1p [Saccharomyces cerevisiae] 1203 72958 0 94 ref|NP_014622.1|High affinity tryptophan and tyrosine HS PP permease, overexpression confers FK506 and FTY720 resistance; Tat2p [Saccharomyces cerevisiae] 1204 77006 1.00E−167 100 ref|NP_182073.1|ATAUR3 (ATAURORA3); ATP binding/ LL LN histone serine kinase(H3-S10 specific)/protein kinase [Arabidopsis thaliana] 1205 74732 0 90 ref|NP_177415.1|casein kinase, putative [Arabidopsis thaliana] CK 1206 74333 1.00E−158 100 ref|NP_180976.1|protein kinase family protein [Arabidopsis HS thaliana] 1207 74735 0 100 ref|NP_173489.2|protein kinase [Arabidopsis thaliana] LN 1208 74736 0 100 ref[NP_176353.1|protein kinase, putative [Arabidopsis thaliana] LL 1209 74737 0 100 gb|AAF16665.1|AC012394_14 putative protein kinase; HS 59396-62219 [Arabidopsis thaliana] 1210 76657 0 95 ref|NP_187827.1|protein kinase family protein SP LL [Arabidopsis thaliana] 1211 76113 0 94 ref|NP_187165.2|protein kinase family protein CS [Arabidopsis thaliana] 1212 74747 0 92 ref[NP_174161.1|protein kinase family protein HS [Arabidopsis thaliana] 1213 77309 0 87 ref|NP_175879.2|protein kinase family protein PEG [Arabidopsis thaliana] 1214 74322 0 94 gb|AAG52342.1|AC011663_21putative protein kinase; LL 29119-30743 [Arabidopsis thaliana] 1215 76212 1.00E−170 93 ref|NP_200959.2|NADP-dependent oxidoreductase, HS LN putative [Arabidopsis thaliana] 1216 76514 1.00E−159 85 ref|NP_568357.1|AAA-type ATPase family protein LL DS [Arabidopsis thaliana] 1217 75242 0 84 ref[NP_200318.1|2-oxoacid dehydrogenase family protein LL [Arabidopsis thaliana] 1218 77324 0 97 gb|AAF79717.1|AC020889_25T1N15.3 PEG LN [Arabidopsis thaliana] 1219 74350 3.00E−95 93 ref|NP_178122.1|APT2 (ADENINE PHOSPHORIBOSYL LN TRANSFERASE 2); adenine phosphoribosyltransferase [Arabidopsis thaliana] 1220 77606 0 96 ref|NP_190925.1|AFC1 (ARABIDOPSIS FUSS- HS SS COMPLEMENTING GENE 1); kinase [Arabidopsis thaliana] 1221 76530 0 92 ref|NP_567069.1|F-box family protein-related HS [Arabidopsis thaliana] 1222 76716 1.00E−86 61 ref|NP_565175.1|RNA recognition motif (RRM)-containing HS protein [Arabidopsis thaliana] 1223 77328 0 89 ref|NP_567904.1|RNA recognition motif (RRM)-containihg HS protein [Arabidopsis thaliana] 1224 12204 0 100 ref|NP_189366.1|G6PD5 (GLUCOSE-6-PHOSPHATE DS DEHYDROGENASE 5); glucose-6-phosphate 1-dehydrogenase [Arabidopsis thaliana] 1225 77011 0 96 ref|NP_563818.1|strictosidine synthase family protein LL [Arabidopsis thaliana] 1226 77607 0 94 ref|NP_175157.1|NRAMP2 (NRAMP metal ion transporter LL PEG 2); metal ion transporter [Arabidopsis thaliana] 1227 74612 1.00E−68 100 ref|NP_177750.1|unknown protein [Arabidopsis thaliana] HS 1228 76126 1.00E−144 100 ref|NP_179467.1|signal recognition particle binding HS [Arabidopsis thaliana] 1229 74376 1.00E−150 95 ref|NP_181340.1|DET2 (DE-ETIOLATED 2) DS [Arabidopsis thaliana] 1230 74377 1.00E−46 100 ref|NP_181546.1|ATEM6 (ARABIDOPSIS EARLY DS LL PEG METHIONINE-LABELLED 6) [Arabidopsis thaliana] 1231 74381 6.00E−63 100 ref|NP_181990.1|mtACP-1 (MITOCHONDRIAL ACYL CARRIER PROTEIN 1); acyl carrier [Arabidopsis thaliana] CS 1232 78364 6.00E−88 87 ref|NP_566062.1|UBC6 (UBIQUITIN-CONJUGATING HS ENZYME 6); ubiquitin-protein ligase [Arabidopsis thaliana] 1233 74623 1.00E−115 75 ref|NP_188379.1|late embryogenesis abundant domain- HS containing protein/LEA domain-containing protein [Arabidopsis thaliana] 1234 74668 1.00E−122 88 ref|NP_188888.1|late embryogenesis abundant protein, DS putative/LEA protein, putative [Arabidopsis thaliana] 1235 74629 5.00E−83 90 ref|NP_566782.1|unknown protein [Arabidopsis thaliana] LL 1236 74635 1.00E−113 92 ref|NP_190864.1|peroxiredoxin type 2, putative CS [Arabidopsis thaliana] 1237 74638 1.00E−100 100 ref|NP_191788.1|ATARFA1E (ADP-ribosylation factor HS SS A1E); GTP binding/phospholipase activator/protein binding [Arabidopsis thaliana] 1238 76721 1.00E−148 77 ref|NP_192093.1|KCO5 (Ca2+ activated outward rectifying PEG K+ channel 5); outward rectifier potassium channel [Arabidopsis thaliana] 1239 78365 2.00E−83 90 ref|NP_568004.1|UBC17 (UBIQUITIN-CONJUGATING CK HS ENZYME 17); ubiquitin-protein ligase [Arabidopsis thaliana] 1240 74655 1.00E−132 91 ref|NP_195437.1|HCF164 (High chlorophyll fluorescence LN 164); thiol-disulfide exchange intermediate [Arabidopsis thaliana] 1241 74660 1.00E−160 92 ref|NP_196119.1|ATTOC34/OEP34 (Translocase of CS PEG chloroplast 34) [Arabidopsis thaliana] 1242 74661 1.00E−180 96 ref|NP_197135.1|ubiquitin carboxyl-terminal hydrolase HS family 1 protein [Arabidopsis thaliana] 1243 75259 1.00E−101 85 ref|NP_198051.1|drought-responsive family protein HS [Arabidopsis thaliana] 1244 75282 3.00E−93 100 ref|NP_201055.1|ATHVA22B (Arabidopsis thaliana HVA22 PEG homologue B) 1245 76724 0 93 ref|NP_173089.1|organic cation transporter-related DS [Arabidopsis thaliana] 1246 12350 1.00E−131 78 gb[AAM61424.1|serine O-acetyltransferase (EC 2.3.1.30) Sat-52 [Arabidopsis thaliana] LN 1247 76522 0 93 ref[NP_001077495.1|unknown protein [Arabidopsis PP thaliana] 1248 77903 0 96 ref|NP_194952.2|protein kinase family protein [Arabidopsis HS LL SS thaliana] 1249 76653 0 100 ref|NP_568860.1|CIPK21 (CBL-INTERACTING PROTEIN CS KINASE 21); kinase [Arabidopsis thaliana] 1250 76524 0 100 ref|NP_199469.1|protein kinase family protein [Arabidopsis CS thaliana] 1251 11356 1.00E−172 100 ref|NP_181165.1|APG10 (ALBINO AND PALE GREEN LN 10); 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxamide isomerase [Arabidopsis thaliana] 1252 75275 0 94 ref|NP_199586.1|protein kinase, putative [Arabidopsis LL thaliana] dbj|BAA01715.1|serine/threonine protein kinase [Arabidopsis thaliana] 1253 76225 0 94 ref|NP_195285.3|CONNEXIN 32; kinase [Arabidopsis PEG thaliana] 1254 75281 0 94 ref|NP_568893.1|protein kinase family protein [Arabidopsis HS thaliana] 1255 74384 1.00E−102 100 ref|NP_175960.1|prenylated rab acceptor (PRA1) family LL protein [Arabidopsis thaliana] 1256 71238 1.00E−168 84 ref|NP_563814.1|DCP1 (DECAPPING 1) [Arabidopsis LN thaliana] 1257 12354 0 100 ref|NP_172738.1|UGE1 (UDP-D-glucose/UDP-D-galactose DS 4-epimerase 1); UDP-glucose 4-epimerase/protein dimerization [Arabidopsis thaliana] 1258 76236 1.00E−157 100 ref|NP_201384.1|leucine-rich repeat family protein HS [Arabidopsis thaliana] 1259 74682 4.00E−83 100 ref[NP_565581.1|unknown protein [Arabidopsis thaliana] CS 1260 73425 0 95 ref|NP_391649.1|transaminase [Bacillus subtilis subsp. LL subtilis str. 168] 1261 73438 0 99 ref|YP_351136. |Glutamate-ammonia ligase SP [Pseudomonas fluorescens PfO-1] 1262 73474 0 92 ref|NP_790236.1|phosphoglycerate kinase [Pseudomonas HS PP syringae pv. tomato str. DC3000] 1263 70850 0 97 ref|NP_190853.1|ATELP1 (VACUOLAR SORTING HS RECEPTOR HOMOLOG) [Arabidopsis thaliana] 1264 73429 1.00E−144 100 ref|ZP_01370194.1|pyrroline-5-carboxylate reductase HS SS CS [Desulfitobacterium hafniense DCB-2] 1265 73441 0 94 ref|ZP_01370604.1|enolase [Desulfitobacterium hafniense PEG DCB-2] 1266 73466 0 97 ref|ZP_00108577.1|COG1063: Threonine dehydrogenase LN and related Zn-dependent dehydrogenases [Nostoc punctiforme PCC 73102] 1267 73455 1.00E−159 100 ref|NP_792905.1|UTP-glucose-1-phosphate HS uridylyltransferase [Pseudomonas syringae pv. tomato str. DC3000] 1268 73432 0 94 ref|YP_582700.1|Alcohol dehydrogenase, zinc-binding CS [Ralstonia metallidurans CH34] 1269 73435 0 97 ref|NP_391271.1|phosphoglyceromutase [Bacillus subtilis LN subsp. subtilis str. 168] 1270 77726 0 99 ref|NP_391273.1|phosphoglycerate kinase [Bacillus subtilis HS subsp. subtilis str. 168] 1271 73483 0 96 ref|NP_009362.1|Pyruvate kinase, functions as a LL homotetramer in glycolysis to convert phosphoenolpyruvate to pyruvate, the input for aerobic (TCA cycle) or anaerobic (glucose fermentation) respiration; Cdc19p [Saccharomyces cerevisiae] 1272 73472 0 99 ref|NP_387397.1|ASPARTATE AMINOTRANSFERASE B DS PROTEIN [Sinorhizobium meliloti 1021] 1273 73526 0 94 ref|NP_242877.1|benzyl alcohol dehydrogenase DS [Bacillus halodurans C-125] 1274 73538 0 100 ref|NP_243126.1|hypothetical protein BH2260 HS [Bacillus halodurans C-125] 1275 73574 1.00E−177 100 ref|NP_244591.1|2-keto-3-deoxygluconate kinase HS [Bacillus halodurans C-125] 1276 73539 1.00E−170 100 ref|NP_287481.1|UTP-glucose-1-phosphate CS uridylyltransferase subunit GalU [Escherichia coli 0157:H7 EDL933] 1277 73563 3.00E−62 90 ref|NP_743010.1|nucleoside diphosphate kinase CK [Pseudomonas putida KT2440] 1278 73575 1.00E−175 100 ref|NP_792508.1|fructokinase [Pseudomonas syringae pv. LL tomato str. DC3000] 1279 73565 0 95 ref|NP_011707.1|High-affinity histidine permease, also HS involved in the transport of manganese ions; H;p1p [Saccharomyces cerevisiae] 1280 73531 0 93 ref|NP_388151.1|hypothetical protein BSU02690 DS [Bacillus subtilis subsp. subtilis str. 168] 1281 73592 0 96 ref|NP_391888.1|6-phosphogluconate dehydrogenase LN [Bacillus subtilis subsp. subtilis str. 168] 1282 74149 0 100 ref|NP_794093.1|pyruvate kinase [Pseudomonas syringae LL pv. tomato str. DC3000] 1283 74174 0 99 ref|NP_416880.1|prediected aminotransferase, PLP- LL LN dependent [Escherichia coli K12] 1284 74151 0 100 ref|NP_417148.1|4-aminobutyrate aminotransferase, PLP- PP dependent [Escherichia coli K12] 1285 74104 0 100 ref)ZP_01369074.1|glucose-1-phosphate CS HS adenylyltransferase [Desulfitobacterium hafniense DCB-2] 1286 74164 0 89 ref|NP_242876.1|aldehyde dehydrogenase DS [Bacillus halodurans C-125] 1287 74129 0 77 ref|YP_001185919.1|methylmalonate-semialdehyde CK dehydrogenase [Pseudomonas mendocina ymp] 1288 72340 0 97 ref|NP_195674.2|GGT1; gamma-glutamyltransferase/ HS glutathione gamma-glutamylcysteinyltransferase [Arabidopsis thaliana] 1289 74155 0 100 ref|NP_385556.1|dihydrolipoamide dehydrogenase HS LL [Sinorhizobium meliloti 1021] 1290 74168 0 87 ref|NP_927730.1|glutathibne reductase [Photorhabdus LN luminescens subsp. laumondii TTO1] 1291 74133 0 96 ref|ZP_00109554.2|COG1249: Pyruvate/2-oxoglutarate HS dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Nostoc punctiforme PCC 73102] 1292 74160 4.00E−95 99 ref|NP_441445.1|hypothetical protein slr0816, LL [Synechocystis sp. PCC 6803] dbj|BAA18125.1|slr0816 [Synechocystis sp. PCC 6803] 1293 74485 0 88 ref|NP_439939.1|hypothetical protein slr1495 HS [Synechocystis sp. PCC 6803] 1294 74450 0 100 ref|NP_442868.1|LIM17 protein [Synechocystis sp. PCC CK 6803] 1295 74487 0 90 ref|NP_357138.2|branched-chain alpha-keto acid PP dehydrogenase subunit E2 [Agrobacterium tumefaciens str. C58] 1296 74406 0 96 gb|AAN78639.1|AE016755_139 Dihydrolipoamide LN dehydrogenase [Escherichia coli CFT073] 1297 74454 1.00E−112 91 ref|NP_927456.1|ribulose-phosphate 3-epimerase LL (pentose-5-phosphate 3-epimerase) (PPE) (R5P3E) [Photorhabdus luminescens subsp. laumondii TTO1] 1298 11361 6.00E−61 83 ref|NP_176291.1|FED A (FERREDOXIN 2); electron LN carrier/iron ion binding [Arabidopsis thaliana] 1299 74431 0 99 ref|NP_390796.1|pyruvate kinase [Bacillus subtilis subsp. HS subtilis str. 168] 1300 74411 0 94 ref|NP_949979.1|fructose-1,6-bisphosphatase SS [Rhodopseudomonas palustris CGA009] 1301 74424 1.00E−172 92 ref|NP_386873.1|PROBABLE FRUCTOSE− PP BISPHOSPHATEALDOLASE CLASS I PROTEIN [Sinorhizobium meliloti 1021] 1302 74525 0 83 ref|NP_931210.1|glutamate synthase subunit beta HS [Photorhabdus luminescens subsp. laumondii TTO1] 1303 74573 1.00E−75 38 ref|YP_720246.1|aspartate aminotransferase LN [Trichodesmium erythraeum IMS101] 1304 75827 2.00E−44 82 ref|NP_565988.1|unknown protein [Arabidopsis thaliana] LL 1305 77329 0 98 ref|NP_566005.1|mitochondrial transcription termination CK factor-related/mTERF-related [Arabidopsis thaliana] 1306 77330 0 97 ref|NP_182296.1|auxin-responsive GH3 family protein PEG [Arabidopsis thaliana] 1307 75830 6.00E−61 100 ref|NP_186754.1|MUB1 (MEMBRANE-ANCHORED CK UBIQUITIN-FOLD PROTEIN 1 PRECURSOR) [Arabidopsis thaliana] 1308 75832 2.00E−42 85 ref|NP_186788.1|VMA10 (VACUOLAR MEMBRANE HS ATPASE 10) [Arabidopsis thaliana] 1309 75836 7.00E−41 73 ref|NP_187208.1|unknown protein [Arabidopsis thaliana] CS 1310 77034 4.00E−28 95 ref|NP_172702.1|unknown protein [Arabidopsis thaliana] HS PP 1311 76255 0 92 ref|NP_566390.1|unknown protein [Arabidopsis thaliana] LL 1312 76542 1.00E−77 69 ref|NP_188337.1|unknown protein [Arabidopsis thaliana] CS LL 1313 77511 0 90 ref|NP_566642.1|unknown protein [Arabidopsis thaliana] SS CK 1314 76261 1.00E−127 86 ref|NP_563649.1|unknown protein [Arabidopsis thaliana] HS 1315 78456 0 97 ref|NP_189202.1|MAP1B (METHIONINE CK AMINOPEPTIDASE 1C); metalloexopeptidase [Arabidopsis thaliana] 1316 77041 1.00E−125 95 ref|NP_189236.3|plastid-lipid associated protein PAP/ LN fibrillin family protein [Arabidopsis thaliana] 1317 76546 0 90 gb|AAF79247.1|AC006917_32F10B6.11 [Arabidopsis LL thaliana] 1318 75848 9.00E−96 100 ref|NP_189535.1|AIG2 (AVRRPT2-1NDUCED GENE 2) CK HS [Arabidopsis thaliana] 1319 77515 0 80 ref[NP_189945.1|zinc knuckle (CCHC-type) family protein HS [Arabidopsis thaliana] 1320 76266 0 82 emb|CAB83070.1|putative protein [Arabidopsis thaliana] PEG 1321 75852 1.00E−26 100 ref|NP_190227.1|unknown protein [Arabidopsis thaliana] HS 1322 76556 0 86 ref[NP_190445.2|zinc finger (DHHC type) family protein PEG [Arabidopsis thaliana] 1323 77523 1.00E−174 96 ref|NP_001078291.1|unknown protein [Arabidopsis HS thaliana] 1324 75863 1.00E−120 100 ref|NP_191267.1|eukaryotic rpb5 RNA polymerase subunit CS family protein [Arabidopsis thaliana] 1325 77052 1.00E−171 96 ref|NP_564000.2|unknown protein [Arabidopsis thaliana] PP 1326 75865 1.00E−56 80 ref|NP_173123.1|ribosomal protein-related [Arabidopsis CS thaliana] 1327 76551 0 92 ref|NP_173144.1|oxido reductase, 2OG-Fe(II) oxygenase PEG family protein [Arabidopsis thaliana] 1328 76280 0 86 ref|NP_564064.1|phytochrome kinase substrate-related LL [Arabidopsis thaliana] 1329 75874 7.00E−96 100 ref|NP_193404.1|glycosyltransferase family protein 28 PP [Arabidopsis thaliana] 1330 75879 9.00E−62 100 ref|NP_194229.1|ATGP4 (Arabidopsis thaliana HS geranylgeranylated protein) 1331 75880 7.00E−59 65 ref|NP_173435.1|unknown protein [Arabidopsis thaliana] HS 1332 77519 1.00E−176 90 ref|NP_196118.1|sad1/unc-84 protein-related [Arabidopsis HS CK thaliana] 1333 76745 1.00E−111 88 dbj|BAB09403.1|unnamed protein product [Arabidopsis HS thaliana] 1334 76554 1.00E−173 91 ref|NP_197092.1|unknown protein [Arabidopsis thaliana] DS 1335 76746 3.00E−93 75 ref|NP_568333.1|unknown protein [Arabidopsis thaliana] CK 1336 76750 1.00E−85 93 ref|NP_197746.1|unknown protein [Arabidopsis thaliana] LL 1337 76621 3.00E−20 100 ref|NP_198912.1|unknown protein [Arabidopsis thaliana] HS 1338 76623 1.00E−23 80 ref|NP_568739.1|unknown protein [Arabidopsis thaliana] LL 1339 76461 1.00E−29 78 gb|AAB86938.1|NOI protein [Arabidopsis thaliana] CS 1340 76462 5.00E−31 100 ref|NP_564277.1|unknown protein [Arabidopsis thaliana] HS PP 1341 78987 1.00E−147 81 ref|NP_201096.1|protein binding/zinc ion binding HS [Arabidopsis thaliana] 1342 76568 0 96 ref|NP_564484.1|unknown protein [Arabidopsis thaliana] HS 1343 76176 0 95 ref|NP_565009.1|glycosyltransferase family 14 protein/ CK core-2/1-branching enzyme family protein [Arabidopsis thaliana] 1344 76177 1.00E−97 100 ref|NP_177287.1|unknown protein [Arabidopsis thaliana] LN 1345 78380 0 100 ref|NP_565058.1|eukaryotic translation initiation factor- LN related [Arabidopsis thaliana] 1346 76629 2.00E−46 100 ref|NP_177894.1|unknown protein [Arabidopsis thaliana] HS 1347 76189 2.00E−58 100 gb|AAD15467.2|unknown protein [Arabidopsis thaliana] CS 1348 76761 1.00E−106 94 ref|NP_179133.1|ATARFB1A (ADP-ribosylation factor LL B1A); GTP binding [Arabidopsis thaliana] 1349 78608 0 100 ref|NP_973624.1|ATORC2/ORC2 (ORIGIN PP RECOGNITION COMPLEX SECOND LARGEST SUBUNIT) [Arabidopsis thaliana] 1350 78115 1.00E−153 100 ref|NP_181669.1|embryo-abundant protein-related CK DS [Arabidopsis thaliana] 1351 74873 0 100 ref|NP_416275.1|glutamate dehydrogenase, NADP- DS specific [Escherichia coli K12] 1352 74826 0 99 ref|NP_416651.1|predicted oxidoreductase [Escherichia HS coli K12] 1353 74850 0 99 gb|AAN81953.1|AE016766_41 D-erythrose 4-phosphate HS dehydrogenase [Escherichia coli CFT073] 1354 74887 4.00E−76 90 gb|AAD25168.1|aquaporin [Saccharomyces cerevisiae] PEG 1355 74804 0 95 gb|EDN59233.1|chromatin remodeling complex member, HS SS PEG RSC [Saccharomyces cerevisiae YJM789] 1356 74831 1.00E−167 81 gb|EAY97794.1|hypothetical protein Osl_019027 [Oryza LN sativa (indica cultivar-group)] 1357 74822 0 69 emb|CA062934.1|unnamed protein product [Vitis vinifera] PEG 1358 74836 1.00E−121 70 ref|NP_187378.1|transcriptional activator, putative LN [Arabidopsis thaliana] 1359 74901 3.00E−31 61 ref|NP_001064928.1|Os10g0491900 [Oryza sativa HS (japonica cultivar-group)] 1360 74974 1.00E−112 87 ref|NP_001063296.1|Os09g0443500 [Oryza sativa HS (japonica cultivar-group)] 1361 74904 1.00E−149 82 ref|NP_001063966.1|Os09g0567900 [Oryza sativa HS (japonica cultivar-group)] 1362 74916 8.00E−92 76 gb]EAZ28333.1|hypothetical protein OsJ_011816 [Oryza PEG sativa (japonica cultivar-group)] 1363 74964 1.00E−158 95 ref|NP_417814.1|predicted phosphoribulokinase LL [Escherichia coli K12] 1364 74918 6.00E−82 82 ref|NP_443015.1|hypothetical protein sll1109 LN [Synechocystis sp. PCC 6803] 1365 74966 0 99 ref |NP_442146.1|hypothetical protein sll0209 HS [Synechocystis sp. PCC 6803] 1366 74979 1.00E−142 82 ref|NP_440823.1|hypothetical protein slr1220 CK LL [Synechocystis sp. PCC 6803] 1367 74934 0 96 ref|YP_350971.1|betaine aldehyde dehydrogenase PEG [Pseudomonas fluorescens PfO-1] 1368 77814 0 92 ref|NP_116585.1|F-box protein required for G1/S and HS G2/M transition, associates with Skp1p and Cdc53p to form a complex, SCFCdc4, which acts as ubiquitin-protein ligase directing ubiquitination of the phosphorylated CDK inhibitor Sic1p; Cdc4p [Saccharomyces cerevisiae] 1369 75387 1.00E−148 53 ref|NP_001067713.1|Os11g0293900 [Oryza sativa CK LL (japonica cultivar-group)] 1370 75328 0 93 ref|NP_001050986.1|Os03g0699200 [Oryza sativa PP (japonica cultivar-group)] 1371 77808 0 74 emb|CA063310.1|unnamed protein product [Vitis vinifera] CS 1372 75389 0 69 ref|NP_00104508.1|Os01g0897100 [Oryza sativa HS (japonica cultivar-group)] 1373 75318 1.00E−126 49 emb|CA040140.1|unnamed protein product [Vitis vinifera] CK 1374 75330 0 70 emb]CAH66847.1|H0525C06.10 [Oryza sativa (indica CS HS cultivar-group)] 1375 75342 1.00E−75 69 ref|NP_001056004.1|Os05g0509700 [Oryza sativa CK (japonica cultivar-group)] 1376 75366 4.00E−59 74 ref|NP_001063106.1|Os09g0397700 [Oryza sativa HS (japonica cultivar-group)] 1377 75319 1.00E−121 73 ref|NP_001050079.1|Os03g0343700 [Oryza sativa HS (japonica cultivar-group)] 1378 75391 0 96 gb|ABU48662.1|G protein alpha subunit [Sorghum bicolor] HS 1379 75334 4.00E−45 92 ref|NP_001049605.1|Os03g0257900 [Oryza sativa HS (japonica cultivar-group)] 1380 75323 0 82 ref|NP_001053032.1|Os04g0466600 [Oryza sativa HS (japonica cultivar-group)] 1381 75396 5.00E−84 77 ref|NP_001068537.1|Os11g0703400 [Oryza sativa PEG (japonica cultivar-group)] 1382 75401 2.00E−72 93 ref|NP_001059557.1|Os07g0454700 [Oryza sativa HS (japonica cultivar-group)] 1383 75413 1.00E−139 90 ref|NP_001050848.1|Os03g0666700 [Oryza sativa LL (japonica cultivar-group)] 1384 75461 0 92 ref|NP_001066463.1|Os12g0236500 [Oryza sativa HS SS PP (japonica cultivar-group)] 1385 75473 6.00E−50 71 ref|NP_001043914.1|Os01g0687600 [Oryza sativa DS (japonica cultivar-group)] 1386 77817 8.00E−26 93 ref|NP_001045143.1]Os01g0908400 [Oryza sativa LL (japonica cultivar-group)] 1387 75416 1.00E−165 81 gb|EAY92384.1|hypothetical protein Osl_013617 [Oryza CK sativa (indica cultivar-group)] 1388 75464 0 68 gb|EAZ22667.1|hypothetical protein OsJ_006150 [Oryza HS sativa (japonica cultivar-group)] 1389 75441 5.00E−46 68 gb|AAA33773.1|PVPR3 LN 1390 75454 2.00E−82 73 ref|NP_001064989.1|Os10g0502000 [Oryza sativa HS (japonica cultivar-group)] 1391 75493 4.00E−31 51 emb|CA048835.1|unnamed protein product [Vitis vinifera] HS PP PEG 1392 75446 2.00E−29 55 gb|ABU54835.1|defender against apoptotic death CS HS [Penaeus monodon] 1393 75495 2.00E−86 82 gb|ABG23395.1|2C-methyl-D-erythritol 2,4- SS cyclodiphosphate synthase [Stevia rebaudiana] 1394 75705 1.00E−102 71 ref|NP_001046126.1|Os02g0187100 [Oryza sativa SP (japonica cultivar-group)] 1395 77818 0 100 ref|NP_241861.1|succinate-semialdehyde dehydrogenase HS PEG [Bacillus halodurans C-125] 1396 75525 0 99 ref|NP_415448.1|aspartate aminotransferase, PLP- LN dependent [Escherichia coli K12] 1397 75549 1.00E−115 37 dbj|BAC10067.1|hypothetical protein [Oryza sativa SS Japonica Group] 1398 75582 0 68 emb|CA016731.1|unnamed protein product [Vitis vinifera] CS PEG 1399 75535 6.00E−53 62 emb|CA018074.1|unnamed protein product [Vitis vinifera] PEG 1400 75547 1.00E−164 74 emb]CA042486.1|unnamed protein product [Vitis vinifera] LL LN 1401 75512 1.00E−141 63 emb|CA040060.1|unnamed protein product [Vitis vinifera] CS HS 1402 75673 1.00E−158 55 ref|NP_001050262.1|Os03g0387900 [Oryza sativa CK (japonica cultivar-group)] 1403 75626 0 78 gb|EAZ07965.1|hypothetical protein Osl_029197 [Oryza HS sativa (indica cultivar-group)] 1404 75674 4.00E−53 66 gb|EAY98259.1|hypothetical protein Osl_019492 [Oryza HS LN sativa (indica cultivar-group)] 1405 75615 2.00E−46 59 gb|EAY75762.1|hypothetical protein Osl_003609 [Oryza CK sativa (indica cultivar-group)] 1406 75627 1.00E−135 92 gb|EAZ15023.1|hypothetical protein OsJ_004848 [Oryza SS sativa (japonica cultivar-group)] 1407 75628 1.00E−103 88 qb|AAQ24835.1|partner of Nob1 [Sorghum bicolor] PEG 1408 75652 1.00E−139 85 gb|EAY93006.1|protein Osl_014239 [Oryza CK sativa (indica cultivar-qroup)] 1409 75605 1.00E−121 55 ref|NP_001047861.1|Os02g0704600 [Oryza sativa CK HS LN (japonica cultivar-group)] 1410 70228 1.00E−83 100 ref|NP 189581.1|AHP2 (HISTIDINE−CONTAINING CK PHOSPHOTRANSMITTER 2); histidine phosphotransfer kinase/signal transducer [Arabidopsis thaliana] 1411 13302 0 95 gb|AAF21885.1A|F101056_1MEI2 [Arabidopsis thaliana] LN 1412 75610 0 86 ref|NP_001054248.1|Os04g0675500 [Oryza sativa CK (japonica cultivar-group)] 1413 75623 0 95 ref|NP 194630.1|AIM1 (ABNORMAL INFLORESCENCE HS MERISTEM); enoyl-CoA hvdratase [Arabidopsis thaliana] 1414 75671 0 88 ref|NP_176918.1|leucine-rich repeat family protein PP [Arabidopsis thaliana] 1415 75695 4.00E−78 63 emb|CA021783.1|unnamed protein product [Vitis vinifera] HS 1416 75648 2.00E−32 46 ref|NP_001054395.1|Os05g0103500 [Oryza sativa SS (japonica cultivar-group)] dbj|BAF16309.1|Os05g0103500 [Oryza sativa (japonica cultivar-group)] 1417 75672 0 84 ref|NP_196925.1|leucine-rich repeat transmembrane PP protein kinase, putative [Arabidopsis thaliana] dbj|BAB08300.1|receptor protein kinase-like protein [Arabidopsis thaliana] 1418 75713 1.00E−141 43 emb|CA021763.1|unnamed protein product [Vitis vinifera] CK 1419 75714 7.00E−35 36 gb|ABK93511.1|unknown [Populus trichocarpa] HS PP 1420 75762 1.00E−171 65 emb|CAN68895.1|hypothetical protein [Vitis vinifera] CK 1421 77954 0 94 ref|NP_172684.1|flavin-containing monooxygenase family HS protein/FMO family protein [Arabidopsis thaliana] 1422 77955 0 95 ref|NP_172680.1|flavin-containlng monooxygenase family HS protein/FMO family protein [Arabidopsis thaliana] 1423 77541 7.00E−85 100 gb|ABK28567.1|unknown [Arabidopsis thaliana] LN 1424 78131 0 93 emb|CAB42923.1|putative mitochondrial protein HS [Arabidopsis thaliana] 1425 78134 6.00E−95 91 ref|NP_192051.2|CBL5 (CALCINEURIN B-LIKE PROTEIN 5) LN SS [Arabidopsis thaliana] 1426 77554 1.00E−138 75 tpg|DAA00869.1|TPA_exp: PDR2 ABC transporter HS [Arabidopsis thaliana] 1427 78992 1.00E−170 90 ref|NP_194508.1|calcium-binding EF hand family protein CK [Arabidopsis thaliana] 1428 77557 0 84 ref|NP_196016.1|IQD12 (IQ-domain 12); calmodulin LL LN binding [Arabidopsis thaliana] 1429 78128 0 96 ref|NP_196397.1|flavin-containing monooxygenase family HS protein/FMO family protein [Arabidopsis thaliana] 1430 77560 0 94 ref|NP_568202.1|calcium-binding EF hand family protein CK HS [Arabidopsis thaliana] 1431 77561 0 100 ref|NP_196694.1|monooxygenase family protein CS CK [Arabidopsis thaliana] 1432 77958 1.00E−108 74 ref|NP_197694.1|TET12 (TETRASPANIN12) PP [Arabidopsis thaliana] 1433 77563 0 92 ref|NP_197887.1|integral membrane transporter family protein CS CK [Arabidopsis thaliana] 1434 78994 0 91 ref|NP_001032056.1|F-box family protein HS [Arabidopsis thaliana] 1435 74508 0 90 ref|NP_850439.1|CYP76C1 (cytochrome P450, family 76, CS HS subfamily C. polypeptide 1); heme binding/iron ion binding/monooxygenase [Arabidopsis thaliana]) 1436 70229 0 100 ref|NP_194337.1|MEK1 (mitogen-activated protein kinase HS kinase 1); MAP kinase kinase/kinase [Arabidopsis thaliana] 1437 77959 0 90 ref|NP_200937.1|flavin-containing monooxygenase family HS protein/FMO family protein [Arabidopsis thaliana] 1438 77567 0 88 ref|NP_171951.2|integral membrane transporter family protein HS LN [Arabidopsis thaliana] 1439 11749 2.00E−52 74 ref|NP_181812.1|PDF1 (PROTODERMAL FACTOR 1) CK [Arabidopsis thaliana] 1440 77578 0 90 ref|NP_180886.1|integral membrane transporter family protein HS [Arabidopsis thaliana] 1441 11751 1.00E−110 90 ref|NP_180871.1|SAR1 (SYNAPTOBREVIN-RELATED LN PROTEIN 1) [Arabidopsis thaliana] 1442 77963 0 86 ref|NP_566652.1|unknown protein [Arabidopsis thaliana] LN 1443 77925 1.00E−149 94 ref|NP_190985.1|ATFIP37 (ARABIDOPSIS THALIANA HS PP FKBP12 INTERACTING PROTEIN 37) [Arabidopsis thaliana] 1444 77927 0 90 ref|NP_564083.1|unknown protein [Arabidopsis thaliana] HS 1445 77345 2.00E−57 100 ref|NP_564113.1|unknown protein [Arabidopsis thaliana] HS 1446 70230 0 96 gb|ABF55662.1|double MYC-tagged mitogen activated HS protein kinase kinase 2 [synthetic construct] 1447 77353 1.00E−65 100 ref|NP_564301.1|unknown protein [Arabidopsis thaliana] HS 1448 77354 6.00E−42 81 ref|NP_564312.1|unknown protein [Arabidopsis thaliana] LL 1449 77355 1.00E−41 90 ref|NP_564515.1|unknown protein [Arabidopsis thaliana] PP 1450 77588 1.00E−152 100 ref|NP_176415.1|unknown protein [Arabidopsis thaliana] CS 1451 77591 1.00E−164 92 ref|NP_565628.1|unknown protein [Arabidopsis thaliana] LL 1452 77594 1.00E−143 72 emb|CAB46003.1|RING-H2 finger protein RHF1a DS [Arabidopsis thaliana] 1453 77595 1.00E−144 71 ref|NP_567661.1|SWIB complex BAF60b domain- LL containing protein [Arabidopsis thaliana] 1454 77364 5.00E−76 84 ref|NP_194770.1|transcription factor [Arabidopsis thaliana] LN 1455 78904 0 100 emb|CAB87764.1|putative protein [Arabidopsis thaliana] HS 1456 77937 0 100 ref|NP_197133.1|acetolactate synthase small subunit, HS putative [Arabidopsis thaliana] 1457 77369 1.00E−103 86 ref|NP_197494.1|plastid-lipid associated protein DS PAP-related/fibrillin-related [Arabidopsis thaliana] 1458 77940 0 89 ref|NP_568648.1|transducin family protein/WD-40 repeat CK HS family protein [Arabidopsis thaliana] 1459 78746 0 100 ref|NP_201387.2|ankyrin repeat family protein [Arabidopsis thaliana] HS 1460 77372 1.00E−119 94 ref|NP_201515.1|F-box family protein [Arabidopsis thaliana] DS 1461 78126 0 86 gb|AAF24593.1|AC007654_9T19E23.14 [Arabidopsis thaliana] CK 1462 77951 0 100 ref|NP_565803.1|ATEYA (ARABIDOPSIS THALIANA LL PEG EYES ABSENT HOMOLOG); protein tyrosine phosphatase, metal-dependent [Arabidopsis thaliana] 1463 75901 0 97 gb|EDN61448.1|F-box protein [Saccharomyces cerevisiae YJM789] CS 1464 12123 1.00E−115 86 ref|NP_196598.1|EMB3010 (EMBRYO DEFECTIVE 3010); LN structural constituent of ribosome [Arabidopsis thaliana] 1465 75987 9.00E−84 80 ref|NP_001105929.1|high affinity nitrate transporter [Zea mays] CS 1466 75940 0 100 ref|NP_842265.1|Phosphoglucose isomerase (PGI) HS PP [Nitrosomonas europaea ATCC 19718] 1467 75919 1.00E−175 95 ref|NP_780153.1|isocitrate dehydrogenase HS LL SS [Xylella fastidiosa Temecula] 1468 75908 0 99 ref|NP 440384.1|glutamate decarboxylase HS [Synechocystis sp. PCC 6803] 1469 75920 0 100 ref|NP_440189.1|ferredoxin-sulfite reductase HS [Synechocystis sp. PCC 6803] 1470 75992 0 94 ref|YP_001636715.1|pyruvate kinase HS [Chloroflexus aurantiacus J-10-fl] 1471 75933 1.00E−116 94 ref|NP_442343.1|ribose-5-phosphate isomerase A HS PP [Synechocystis sp. PCC 6803] 1472 77965 0 92 ref|NP_181991.1|kelch repeat-containing F-box family protein DS [Arabidopsis thaliana] 1473 77966 0 89 ref|NP_186818.1|unknown protein [Arabidopsis thaliana] LN 1474 77972 0 90 ref|NP_189657.1|unknown protein [Arabidopsis thaliana] HS 1475 78522 0 96 ref|NP_175744.1|unknown protein [Arabidopsis thaliana] SP 1476 12194 3.00E−78 91 ref|NP_176772.1|TPX2 (THIOREDOXIN-DEPENDENT CK PEROXIDASE 2); antioxidant [Arabidopsis thaliana] 1477 78525 0 87 gb|AAC24050.1|Similar to S. cerevisiae SIK1P protein LN 1478 78527 0 87 gb|AAC18814.1|Contains homology to serine/threonine PEG protein kinase gb|X99618 from Mycobacterium tuberculosis. 1479 78917 0 95 ref|NP_177258.3|armadillo/beta-catenin repeat family protein/U-box LN domain-containing protein [Arabidopsis thaliana] 1480 78920 0 100 ref|NP_565146.1|ACR3 (ACT Domain Repeat 3) [Arabidopsis thaliana] PP 1481 78535 0 96 ref|NP_179324.2|pantothenate kinase-related [Arabidopsis thaliana] CK 1482 78538 0 98 ref|NP_180538.1|kelch repeat-containing F-box family protein HS [Arabidopsis thaliana] 1483 78922 0 95 ref|NP_181393.1|F-box family protein [Arabidopsis thaliana] HS PP CS 1484 77984 1.00E−109 100 ref|NP_566068.1|unknown protein [Arabidopsis thaliana] LN CK 1485 73938 0 100 ref|NP_201190.1|AAP4 (amino acid permease 4); DS CS amino acid permease [Arabidopsis thaliana] 1486 78621 0 100 gb|AAD13704.1|hypothetical protein [Arabidopsis thaliana] HS 1487 77990 1.00E−74 85 ref|NP_187290.1|integral membrane family protein DS [Arabidopsis thaliana] 1488 78386 1.00E−132 100 ref|NP_187319.1|peptidyl-prolyl cis-trans isomerase SP cyclophilin-type family protein [Arabidopsis thaliana] 1489 78001 1.00E−70 100 gb|AAF23196.1|AC016795_9 unknown protein HS [Arabidopsis thaliana] 1490 78543 0 90 ref|NP_187807.1|S-locus related protein SLR1, putative (S1) HS [Arabidopsis thaliana] 1491 78002 1.00E−136 100 ref|NP_187847.1|unknown protein [Arabidopsis thaliana] LL 1492 12259 1.00E−134 100 gb|AAM67061.1|ribosomal protein S2, putative [Arabidopsis thaliana] LN 1493 78005 3.00E−93 96 ref|NP_172796.1|unknown protein [Arabidopsis thaliana] LL 1494 78008 1.00E−135 88 ref|NP_188459.1|unknown protein [Arabidopsis thaliana] PEG 1495 78019 1.00E−176 94 ref|NP_001031574.1|unknown protein [Arabidopsis thaliana] CK HS 1496 78020 2.00E−74 89 gb|ABK28619.1|unknown [Arabidopsis thaliana] SS 1497 78023 1.00E−121 94 ref|NP_173373.2|unknown protein [Arabidopsis thaliana] DS 1498 78548 1.00E−146 86 ref|NP_564100.1|abscisic acid-responsive HVA22 family protein LN PP [Arabidopsis thaliana] 1499 78161 1.00E−103 94 ref|NP_173738.2|caleosin-related family protein HS PEG [Arabidopsis thaliana] 1500 78162 1.00E−179 100 ref|NP_564270.1|unknown protein [Arabidopsis thaliana] CK LN PP PEG 1501 78033 1.00E−148 90 ref|NP_564297.1|unknown protein [Arabidopsis thaliana] LL 1502 78622 0 95 ref|NP_564315.1|unknown protein [Arabidopsis thaliana] CK 1503 78036 1.00E−67 100 ref|NP_174257.1|unknown protein [Arabidopsis thaliana] DS 1504 78043 0 96 ref|NP_175182.2|endonuclease/exonuclease/phosphatase family CS protein [Arabidopsis thaliana] 1505 78165 2.00E−92 84 ref|NP_564788.1|unknown protein [Arabidopsis thaliana] LL 1506 78066 1.00E−116 86 gb|AAF68106.1|AC010793_1 F20B17.2 [Arabidopsis thaliana] PP 1507 78069 1.00E−124 64 ref|NP_178248.2|pentatricopeptide (PPR) repeat-containing protein PP [Arabidopsis thaliana] 1508 78183 1.00E−115 100 ref|NP_180390.2|unknown protein [Arabidopsis thaliana] PP 1509 78170 2.00E−37 100 qb|AAS47599.1|At2g33690 [Arabidopsis thaliana] PP 1510 78953 1.00E−125 88 ref|NP_565921.1|unknown protein [Arabidopsis thaliana] PP 1511 78929 0 97 ref|NP_182026.1|CCD7 (more axillary growth 3) LN [Arabidopsis thaliana] 1512 78564 1.00E−63 100 ref|NP_188669.1|unknown protein [Arabidopsis thaliana] PEG 1513 78566 0 100 ref|NP_566813.1|unknown protein [Arabidopsis thaliana] HS 1514 78591 0 96 gb|AAG12668.1|AC027033_3hypothetical protein; 23726-25026 SS [Arabidopsis thaliana] 1515 78181 3.00E−99 100 ref|NP_563968.1|unknown protein [Arabidopsis thaliana] LN 1516 78190 2.00E−30 71 ref|NP_564173.1|unknown protein [Arabidopsis thaliana] LL 1517 78571 0 93 gb|AAF79874.1|AC000348_27T7N9.16 [Arabidopsis thaliana] CK 1518 78933 1.00E−107 84 gb|AAG51731.1|AC068667_10hypothetical protein; LN 69078-67980 [Arabidopsis thaliana] 1519 78573 8.00E−73 80 ref|NP_174417.1|LOB domain protein 4/lateral organ boundaries CK domain protein 4 (LBD4) [Arabidopsis thaliana] 1520 78632 0 100 ref|NP_564507.1|unknown protein [Arabidopsis thaliana] HS LL PP 1521 78959 0 100 ref|NP_175985.1|pentatricopeptide (PPR) repeat-containing protein LN [Arabidopsis thaliana] 1522 78191 3.00E−51 63 ref|NP_564986.1|ribosomal protein L12 family protein HS LN [Arabidopsis thaliana] 1523 78595 1.00E−150 92 gb|AAB70396.1|Similar to ATP-dependent Clp protease (gb|D90915). HS PEG 1524 78646 0 100 ref|NP_172453.1|pentatricopeptide (PPR) repeat-containing protein HS [Arabidopsis thaliana] 1525 76325 1.00E−143 82 gb|EAY88291.1|hypothetical protein Osl_009524 CS [Oryza sativa (indica cultivar-group)] 1526 76337 6.00E−76 87 ref|NP_001053732.1|Os04g0595200 HS [Oryza sativa (japonica cultivar-group)] 1527 76349 1.00E−139 56 ref|NP_001066102.1|Os12g0136200 PP [Oryza sativa (japonica cultivar-group)] 1528 76302 4.00E−75 82 ref|NP_001047161.1|Os02g0564500 LL [Oryza sativa (japonica cuttivar-group)] 1529 76329 0 92 ref|NP_014151.1|RNA polymerase I subunit A49; Rpa49p PEG PP [Saccharomyces cerevisiae] 1530 76353 0 97 ref|NP_010937.1|Nucleotide binding alpha subunit of the SS heterotrimeric G protein that interacts with the receptor Gpr1p, has signaling role in response to nutrients; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; Gpa2p [Saccharomyces cerevisiae] 1531 76389 0 83 ref|NP_014172.1|Co-chaperone that stimulates the CK ATPase activity of Ssa1p, required for a late step of ribosome biogenesis; associated with the cytosolic large ribosomal subunit; contains a J-domain; mutation causes defects in fluid-phase endocytosis; Jjj1p [Saccharomyces cerevisiae] 1532 76378 1.00E−119 79 ref|NP 014726.1|Repressor of G1 transcription that binds HS PEG to SCB binding factor (SBF) at SCB target promoters in early G1; phosphorylation of Whi5p by the CDK, Cln3p/Cdc28p relieves repression and promoter binding by Whi5; periodically expressed in G1; Whi5p [Saccharomyces cerevisiae] 1533 76392 1.00E−59 55 ref|NP_001045725.1|Os02g0122300 LL [Oryza sativa (japonica cultivar-group)] 1534 76321 0 76 ref|NP_001058970.1|Os07g0166100 LN [Oryza sativa (japonica cultivar-qroup)] 1535 76345 0 86 ref|NP_001043794.1|Os01g0665200 DS [Oryza sativa (japonica cultivar-group)] 1536 76381 0 88 ref|NP_001058289.1|Os06g0663200 HS [Oryza sativa (japonica cultivar-group)] 1537 76358 0 76 ref|NP_001050845.1|Os03g0666200 LN [Oryza sativa (japonica cultivar-group)] 1538 12629 0 97 ref|NP_194110.2|unknown protein [Arabidopsis thaliana] HS 1539 76335 1.00E−101 66 ref|NP_001065630.1|Os11g0127700 LL [Oryza sativa (japonica cultivar-group)] 1540 76372 0 82 gb|EAY93387.1|hypothetical protein Osl_014620 PP [Oryza sativa (indica cultivar-group)] 1541 76396 0 57 ref|NP_001047355.1|Os02g0602100 DS [Oryza sativa (japonica cultivar-group)] 1542 72314 0 92 ref|NP_187714.1|steroid hormone receptor/ HS transcription factor [Arabidopsis thaliana] 1543 77840 1.00E−166 87 ref|NP_001066296.1|Os12g0176500 CS CK [Oryza sativa (japonica cultivar-group)] 1544 76886 1.00E−143 85 dbj|BAC99390.1|putative U3 snoRNP protein IMP4 PP PEG [Oryza sativa Japonica Group] 1545 76803 1.00E−163 90 gb|EAY89818.1|hypothetical protein Osl_011051 LL [Oryza sativa (indica cultivar-group)] 1546 10302 0 97 ref|NP_172288.1|ATNRT2:1 (Arabidopsis thaliana high HS affinity nitrate transporter 2.1); nitrate transporter 1547 71107 0 96 ref|NP_030560.1|unknown protein [Arabidopsis thaliana] HS 1548 76887 0 86 ref|NP_001044302.1|Os01g0758400 HS PP PEG [Oryza sativa (japonica cultivar-group)] 1549 77842 0 76 ref|NP_001047779.1|Os02g0688500 LN [Oryza sativa (japonica cultivar-group)] 1550 76805 1.00E−165 85 dbj|BAD08085.1|putative ornithine carbamoyltransferase HS [Oryza sativa (japonica cultivar-group)] 1551 76817 2.00E−51 78 ref|NP_001063927.1|Os09g0560500 HS [Oryza sativa (japonica cultivar-group)] 1552 77843 1.00E−68 66 ref|NP_001053206.1|Os04g0497400 CS [Oryza sativa (japonica cultivar-group)] 1553 77844 0 94 ref|NP_001105843.1|sialytransferase like protein PP [Zea mays] 1554 76890 0 98 ref|NP_001044001.1|Os01g0703600 HS [Oryza sativa (japonica cultivar-group)] 1555 77839 1.00E−155 74 ref|NP_001047096.1|Os02g0550700 DS PP [Oryza sativa (japonica cultivar-group)] 1556 76868 0 83 ref|NP_001052270.1|Os04g0223000 HS PP PEG CS [Oryza sativa (japonica cultivar-group)] 1557 76821 1.00E−144 80 ref|NP_001042197.1|Os01g0179200 LN [Oryza sativa (japonica cultivar-group)] 1558 76869 3.00E−98 73 gb|EAZ29350.1|hypothetical protein OsJ_012833 HS PP [Oryza sativa (japonica cultivar-group)] 1559 76881 0 88 ref|NP_001049165.1|Os03g0180700 PP [Oryza sativa (japonica cultivar-group)] 1560 76894 4.00E−33 94 ref|NP_001066312.1|Os12g0180400 LN [Oryza sativa (japonica cultivar-group)] 1561 11930 0 100 dbj|BAF01049.1|hypothetical protein [Arabidopsis thaliana] SS 1562 76848 2.00E−80 90 ref|NP_00143542.1|Os01g0610100 HS [Oryza sativa (japonica cultivar-group)] 1563 76901 2.00E−44 85 gb|EAY92619.1|hypothetical protein Osl_013852 LN [Oryza sativa (indica cultivar-group)] 1564 76914 1.00E−139 78 gb|EAY79090.1|hypothetical protein Osl_033049 PP [Oryza sativa (indica cultivar-group)] 1565 76939 1.00E−137 71 gb|EAY98958.1|hypothetical protein Osl_020191 CK [Oryza sativa (indica cultivar-group)] 1566 76987 1.00E−150 72 gb|ABF93996.1|integral membrane protein DUF6 CK containing protein, expressed [Oryza sativa (japonica cultivar-group)] 1567 76804 4.00E−58 76 gb|EAZ05371.1|hypothetical protein Osl_026603 HS LN [Oryza sativa (indica cultivar-group)] 1568 76941 4.00E−26 69 gb|EAY83408.1|hypothetical protein Osl_037367 HS [Oryza sativa (indica cultivar-group)] 1569 77113 0 58 ref|NP_001064033.1|Os10g0110600 PEG [Oryza sativa (japonica cultivar-group)] 1570 77185 0 80 dbj|BAD45738.1|thiF family protein-like DS [Oryza sativa Japonica Group)] 1571 12911 0 100 ref|NP_001078414.1|binding [Arabidopsis thaliana] LN HS 1572 77127 0 89 ref|NP_001062585.1|Os09g0115600 HS PEG [Oryza sativa (japonica cultivar-group)] 1573 77177 0 85 gb|EAY84671.1|hypothetical protein Osl_005904 PEG [Oryza sativa (indica cultivar-group)] 1574 77178 0 100 ref|NP_441510.1|bifunctional 3,4-dihydroxy-2- HS butanone 4-phosphate synthase/GTP cyclohydrolase II protein [Synechocystis sp. PCC 6803] 1575 77179 2.00E−15 60 gb|EAY74575.1|hypothetical protein Osl_002422 HS [Oryza sativa (indica cultivar-group)] 1576 77191 8.00E−61 81 ref|NP_001046564.1|Os02g0282100 PP [Oryza sativa (japonica cultivar-group)] 1577 77145 2.00E−48 81 ref|NP_001051289.1|Os03g0751000 CK PP [Oryza sativa (japonica cultivar-group)] 1578 77169 1.00E−137 87 gb|AAP50960.11putative aurora-related kinase PP [Oryza sativa (japonica cultivar-group)] 1579 77110 5.00E−30 56 ref|NP_001042508.1|Os01g0233000 LL LN [Oryza sativa (japonica cultivar-group)] 1580 77146 0 100 ref|NP_353311.1|bifunctional GMP synthase/ PP glutamine amidotransferase protein [Agrobacterium tumefaciens str. C58] 1581 77170 7.00E−59 82 emb|CAH67592.1|OSIGBa0092M08.4 DS [Oryza sativa (indica cultivar-qroup)] 1582 77171 0 95 ref|NP_244906.1|potassium/proton antiporter HS [Bacillus halodurans C-125] 1583 77148 0 100 ref|NP_661081.1|bifunctional GMP synthase/ CK glutamine amidotransferase protein [Chlorobium tepidum TLS] 1584 11933 1.00E−149 94 ref|NP 849952.1|GONST1 (GOLGI LN NUCLEOTIDE SUGAR TRANSPORTER 1) [Arabidopsis thaliana] 1585 77160 0 87 ref|NP 414589.1|potassium: proton antiporter DS [Escherichia coli K12] 1586 77172 0 92 gb|AAC77846.1|mannose-1-P guanosyltransferase LL [Escherichia coli] 1587 77184 0 92 ref|NP_243321.1|flagellum-specific ATP synthase HS [Bacillus halodurans C-125] 1588 77225 0 94 ref|NP_662474.1|3,4-dihydroxy-2-butanone 4-phosphate LL synthase/GTP cyclohydrolase II [Chlorobium tepidum TLS] 1589 77250 0 97 ref|NP_599940.1|detergent sensitivity rescuer dtsR1 LN [Corynebacterium glutamicum ATCC 13032] 1590 77277 0 95 ref|NP_001048987.1|Os03g0151800 DS [Oryza sativa (japonica cultivar-group)] ica cultivar-group)] 1591 77245 7.00E−45 64 gb|EAY86480.1|hypothetical protein Osl_007713 SS [Oryza sativa (indica cultivar-group)] 1592 77246 4.00E−49 98 gb|EAZ21400.1|hypothetical protein OsJ_004883 HS [Oryza sativa (japonica cultivar-group)] 1593 77462 0 75 ref|NP_001065111.1|Os10g0525000 CK [Oryza sativa (japonica cultivar-group)] 1594 77414 0 82 ref|NP_001046919.1|Os02g0506500 HS [Oryza sativa (japonica cultivar-group)] 1595 77439 0 82 ref|NP_001045101.1|Os01g0899500 PEG [Oryza sativa (japonica cultivar-group)] 1596 77463 1.00E−106 89 ref|NP_001048776.1|Os03g0119000 HS [Oryza sativa (japonica cultivar-group)] 1597 77488 0 80 gb|EAT84267.1|hypothetical protein SNOG_07991 DS [Phaeosphaeria nodorum SN15] 1598 77441 5.00E−87 82 ref|NP_001053804.1|Os04g0606900 SS PEG [Oryza sativa (japonica cultivar-group)] 1599 77464 1.00E−164 90 gb|EAT77502.1|hypothetical protein SNOG_14959 PEG [Phaeosphaeria nodorum SN15] 1600 77442 0 83 ref|NP_013943.1|SR protein kinase (SRPK) involved HS in regulating proteins involved in mRNA metabolism and cation homeostasis; similar to human SRPK1; Sky1p [Saccharomyces cerevisiae] 1601 77419 0 100 ref|NP_191311.1|ATSIP2 (ARABIDOPSIS THALIANA CK HS SEED IMBIBITION 2); hydrolase, hydrolyzing O-glycosyl compounds [Arabidopsis thaliana] 1602 12444 1.00E−146 100 ref|NP_569036.1|GAMMA CA3 (GAMMA LN CARBONIC ANHYDRASE 3); carbonate dehydratase [Arabidopsis thaliana] 1603 11791 0 87 ref|NP_188619.2|phototropic-responsive NPH3 family protein LN [Arabidopsis thaliana] 1603 12445 0 87 ref|NP_188619.2|phototropic-responsive NPH3 family protein HS [Arabidopsis thaliana] 1604 71249 0 96 ref|NP_189251.1|CYP71B22 (cytochrome P450, family 71, HS subfamily B, polypeptide 22); oxygen binding [Arabidopsis thaliana] 1605 71237 0 95 ref|NP_192740.1|short-chain dehydrogenase/reductase CK (SDR) family protein [Arabidopsis thaliana] 1606 12315 1.00E−97 100 ref|NP_567911.1|unknown protein [Arabidopsis thaliana] DS gb|AAM66960.1|unknown [Arabidopsis thaliana] 1606 12366 1.00E−97 100 ref|NP_567911.1|unknown protein [Arabidopsis thaliana] DS gb|AAM66960.1|unknown [Arabidopsis thaliana]

Trait Enhancement Screens

DS-Enhancement of drought tolerance identified by a soil drought stress tolerance screen: Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage. The drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting. The present invention provides recombinant DNA that can improve the plant, survival rate under such sustained drought condition. Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant DNA can find particular use in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle. As demonstrated from the model plant screen, in some embodiments of transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.

PEG-Enhancement of drought tolerance identified by PEG induced osmotic stress tolerance screen: Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits et al., (1995) Plant Physiol. 107:125-130). Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution. Thus, a PEG-induced osmotic stress tolerance screen can be a surrogate for drought tolerance screen. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.

SS-Enhancement of drought tolerance identified by high salinity stress tolerance screen: Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, and (3) toxic effects caused by the salt ions, e.g., inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought. The present invention provides genes that help plants maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with enhanced drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to control plants.

HS-Enhancement of drought tolerance identified by heat stress tolerance screen: Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified by the present invention as heat stress tolerance conferring genes can also impart enhanced drought tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.

CK and CS-Enhancement of tolerance to cold stress: Low temperature can immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential. In the present invention, two screening conditions, e.g., cold shock tolerance screen (CK) and cold germination tolerance screen (CS), were set up to look for transgenic plants that display visual growth advantage at lower temperature. In cold germination tolerance screen, the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating. The trait-improving recombinant DNA identified by such screen can be used for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants. In cold shock tolerance screen, the transgenic plants were first grown under the normal growth temperature of 22° C. until day 8 post plating, and subsequently were placed under 8° C. until day 28 post plating. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.

Enhancement of tolerance to multiple stresses: Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, e.g., multiple stress tolerance genes, the plant can be enabled to react to different kinds of stresses. For examples, PEP SEQ ID NO: 1000 can be used to enhance both salt stress tolerance and heat stress tolerance in plants. Of particular interest, plants transformed with PEP SEQ ID NO: 1495 can resist salt and heat stress. Plants transformed with PEP SEQ ID NO: 1483 can also improve growth in early stage and under heat stress. In addition to these multiple stress tolerance genes, the stress tolerance conferring genes provided by the present invention can be used in combinations to generate transgenic plants that can resist multiple stress conditions.

PP-Enhancement of early plant growth and development: It has been known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy and vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential. Traditionally early planting and applying fertilizer are the methods used for promoting early seedling vigor. In early development stage, plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems that continuously generate new organs throughout post-embryonic development. “Early growth and development” used herein encompasses the stages of seed imbibition through the early vegetative phase. The present invention provides genes that can be used to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions. The transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling. Furthermore, seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants can also be used to generate transgenic plants that are more resistant to various stress conditions due to enhanced early plant development. The present invention provides such exemplary recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g., PEP SEQ ID NO: 1043 which can improve the plant early growth and development, and impart heat stress tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.

SP-Enhancement of late plant growth and development: “Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity. In certain embodiments, transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3, exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length. On one hand, the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant. On the other hand, the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have enhanced development during leaf development and seed maturation providing a higher to yield potential as compared to control plants.

LL-Enhancement of tolerance to shade stress identified in a low light screen: The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased. As the result, a plant under low light condition increases significantly its stem length at the expanse of leaf, seed or fruit and storage organ development, thereby adversely affecting of yield. The present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants. The transgenic plants generated by the present invention can be suitable for a higher density planting, thereby resulting increased yield per unit area.

LN-Enhancement of Tolerance to Low Nitrogen Availability Stress

Nitrogen is a key factor in plant growth and crop yield. The metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves. All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.

According to the present invention, transgenic plants generated using the recombinant nucleotides, which confer enhanced nitrogen use efficiency, identified as such in Table 3, exhibit one or more desirable traits including, but not limited to, increased seedling weight, greener leaves, increased number of rosette leaves, increased or decreased root length. One skilled in the art can recognize that the transgenic plants provided by the present invention with enhanced nitrogen use efficiency can also have altered amino acid or protein compositions, increased yield and/or better seed quality. The transgenic plants of the present invention can be productively cultivated under low nitrogen growth conditions, e.g., nitrogen-poor soils and low nitrogen fertilizer inputs, which would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless. The transgenic plants also can be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.

Stacked Traits: The present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an enhanced phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready® trait, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Explementary herbicides include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides. To illustrate that the production of transgenic plants with herbicide resistance is a capability of those of ordinary skill in the art, reference is made to U.S. patent application publications 2003/0106096A1 and 2002/0112260A1 and U.S. Pat. Nos. 5,034,322; 5,776,760, 6,107,549 and 6,376,754, all of which are incorporated herein by reference. To illustrate that the production of transgenic plants with pest resistance is a capability of those of ordinary skill in the art reference is made to U.S. Pat. Nos. 5,250,515 and 5,880,275 which disclose plants expressing an endotoxin of Bacillus thuringiensis bacteria, to U.S. Pat. No. 6,506,599 which discloses control of invertebrates which feed on transgenic plants which express dsRNA for suppressing a target gene in the invertebrate, to U.S. Pat. No. 5,986,175 which discloses the control of viral pests by transgenic plants which express viral replicase, and to U.S. Patent Application Publication 2003/0150017 A1 which discloses control of pests by a transgenic plant which express a dsRNA targeted to suppressing a gene in the pest, all of which are incorporated herein by reference.

Once one recombinant DNA has been identified as conferring an enhanced trait of interest in transgenic Arabidopsis plants, several methods are available for using the sequence of that recombinant DNA and knowledge about the protein it encodes to identify homologs of that sequence from the same plant or different plant species or other organisms, e.g., bacteria and yeast. Thus, in one aspect, the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 803, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 804 to SEQ ID NO: 1606. In another aspect, the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 1607 through SEQ ID NO: 94613. In yet another aspect, the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.

The trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with enhanced traits provided by the present invention are not limited to any particular plant species. Indeed, the plants according to the present invention can be of any plant species, e.g., can be monocotyledonous or dicotyledonous. In one embodiment, they are agricultural plants, e.g., plants cultivated by man for purposes of food production or technical, particularly industrial applications. Of particular interest in the present invention are corn and soybean plants. The recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention. Other plants of interest in the present invention for production of transgenic plants having enhanced traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.

In certain embodiments, the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly enhanced traits as the transgenic Arabidopsis counterpart. Enhanced physiological properties in transgenic plants of the present to invention can be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect enhanced responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions. Biomass measures can be made on greenhouse or field grown plants and can include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.

Trait data on morphological changes can be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil. Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker, stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other enhanced traits can be identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance. In addition, trait characteristics of harvested grain can be confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.

To confirm hybrid yield in transgenic corn plants expressing genes of the present invention, it can be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Illinois or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.

Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein. Plant parts for these purposes can include leaves, stems, roots, flowers, tissue's, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture. Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.

The various aspects of the invention are illustrated by means of the following examples which are in no way intended to limit the full breath and scope of claims.

EXAMPLES Example 1 Identification of Recombinant DNA that Confers Enhanced Trait(s) to Plants A. Plant Expression Constructs for Arabidopsis Transformation

Each gene of interest was amplified from a genomic or cDNA library using primers specific to sequences upstream and downstream of the coding region. Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, et al., PNAS 95:376-381, 1998; Guyer, e.g., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577). The transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide. The transformation of Arabidopsis plants was carried out using the vacuum infiltration method known in the art (Bethtold, et al., Methods Mol. Biol. 82:259-66, 1998). Seeds harvested from the plants, named as T1 seeds, were subsequently grown in a glufosinate-containing selective medium to select for plants which were actually transformed and which produced T2 transgenic seed.

B. Soil Drought Tolerance Screen

This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions

T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA). Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 μmol/m²/s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.

To identify drought tolerant plants, plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.

At the end of this assay, seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.

Two approaches were used for statistical analysis on the wilting response. First, the risk score was analyzed for wilting phenotype and treated as a qualitative response according to the example 1L. Alternatively, the survival analysis was carried out in which the proportions of wilted and non-wilted transgenic and control plants were compared over each of the six days under scoring and an overall log rank test was performed to compare the two survival curves using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). A list of recombinant DNA constructs which improve drought tolerance in transgenic plants is illustrated in Table 4

TABLE 4 PEP Drought score Seed yield SEQ Construct Delta P- Delta P- ID ID Orientation mean value mean value 989 10471 SENSE 0.069 0.285 0.368 0.021 1224 12204 SENSE 0.152 0.018 −0.519 0.041 1606 12315 ANTI-SENSE 0.067 0.029 −0.126 0.210 1257 12354 ANTI-SENSE 0.118 0.334 −0.663 0.001 1606 12366 SENSE −0.105 0.735 −0.072 0.403 852 13623 SENSE 0.309 0.005 −0.202 0.403 812 13638 ANTI-SENSE 0.195 0.047 −0.930 0.045 838 13811 SENSE −0.037 0.729 −0.578 0.032 860 14248 SENSE 0.205 0.013 −0.484 0.066 885 14910 ANTI-SENSE −0.087 0.305 −0.261 0.220 891 14932 ANTI-SENSE 0.222 0.011 −0.019 0.957 879 15111 ANTI-SENSE 0.082 0.241 0.624 0.019 893 15964 ANTI-SENSE 0.003 0.023 −0.396 0.028 899 15986 ANTI-SENSE 0.199 0.128 −0.022 0.773 900 15987 ANTI-SENSE 0.223 0.416 −0.156 0.576 904 15995 ANTI-SENSE 0.281 0.196 −0.362 0.157 945 16614 SENSE 0.136 0.001 0.059 0.440 959 19162 SENSE 0.007 0.887 0.348 0.019 999 19423 SENSE 0.222 0.024 −0.460 0.069 1003 19425 SENSE 0.002 0.556 0.099 0.019 1081 71667 SENSE 0.064 0.790 −0.314 0.101 1164 72717 SENSE 0.043 0.031 −0.173 0.221 1165 72718 SENSE 0.119 0.037 −0.272 0.359 1167 72779 SENSE −0.026 0.491 0.395 0.006 1168 72791 SENSE 0.284 0.046 −1.867 0.009 1272 73472 SENSE 0.159 0.036 −0.223 0.511 1273 73526 SENSE −0.219 0.141 −0.250 0.145 1280 73531 SENSE −0.277 0.022 −0.097 0.740 1132 73738 SENSE 0.386 0.022 −1.025 0.018 1485 73938 SENSE 0.117 0.050 0.309 0.052 1069 74060 SENSE 0.116 0.016 0.195 0.200 1286 74164 SENSE 0.602 0.031 0.287 0.137 1157 74257 SENSE −0.139 0.622 −0.366 0.059 1146 74269 SENSE 0.176 0.057 −0.101 0.273 1229 74376 SENSE −0.023 0.583 −0.747 0.053 1234 74668 SENSE 0.112 0.018 −0.931 0.063 1351 74873 SENSE 0.256 0.006 0.110 0.627 1385 75473 SENSE 0.108 0.031 −1.469 0.015 1535 76345 SENSE −0.024 0.476 0.318 0.017 1541 76396 SENSE −0.146 0.218 −0.137 0.518 1245 76724 SENSE 0.514 0.029 −1.467 0.021 1581 77170 SENSE 0.258 0.026 −0.436 0.026 1570 77185 SENSE 0.180 0.037 −0.602 0.086 1457 77369 SENSE −0.117 0.194 −0.324 0.096 1460 77372 SENSE 0.623 0.017 −0.108 0.028 1597 77488 SENSE 0.001 0.973 −0.252 0.075 1452 77594 SENSE 0.200 0.032 −0.334 0.096 1555 77839 SENSE 0.082 0.021 −0.242 0.298 1472 77965 SENSE 0.643 0.003 −0.157 0.456 1487 77990 SENSE 0.246 0.022 −0.303 0.458 1497 78023 SENSE 0.364 0.004 −3.072 0.012 1503 78036 SENSE 0.651 0.010 −0.959 0.095 1350 78115 SENSE 0.412 0.027 −0.024 0.880 1061 78321 SENSE 0.254 0.044 −0.941 0.014 1230 74377 SENSE 0.327 0.028 / / 1007 70419 SENSE 0.007 0.047 −0.599 0.012 Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 1047, 1073, 1105, 1106, 1137, 1190, 1216, 1334, 1585, or 1590 showed enhanced drought tolerance by the second criteria as illustrated in Example 1L.

C. Heat Stress Tolerance Screen

Under high temperatures, Arabidopsis seedlings become chlorotic and root growth is inhibited. This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.

T2 seeds were plated on ½× MS salts, 1% phytagel, with 10 μg/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ˜140 μmol/m²/s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, et al., (2001) The Plant Cell 13, 1499-1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve heat tolerance in transgenic plants illustrated in Table 5.

TABLE 5 Growth stage Root length at day 14 Seedling PEP Con- day 14 Risk weight SEQ struct Orien- Delta P- score P- Delta P- ID ID tation mean value mean value mean value 848 10706 ANTI- −0.080 0.577 −0.056 0.371 0.423 0.023 SENSE 822 13231 SENSE 0.267 0.037 1.633 0.010 1.492 0.000 834 13914 SENSE 0.283 0.096 0.466 0.230 1.497 0.016 827 15606 SENSE −0.107 0.459 0.032 0.889 0.658 0.049 876 15623 SENSE 0.265 0.088 0.150 0.371 1.064 0.012 906 16213 SENSE 0.020 0.917 0.048 0.579 0.681 0.013 943 16603 SENSE 0.171 0.300 0.783 0.192 0.994 0.035 941 16617 SENSE 0.327 0.055 0.179 0.312 1.362 0.007 934 17502 SENSE −0.082 0.580 0.989 0.402 0.519 0.026 935 17503 SENSE 0.149 0.052 0.015 0.828 0.697 0.003 897 18203 SENSE −0.078 0.640 −0.221 0.300 0.728 0.041 984 18238 SENSE 0.031 0.845 −0.077 0.457 0.820 0.047 853 18302 SENSE 0.315 0.074 1.298 0.269 1.271 0.011 851 18304 SENSE 0.346 0.222 0.374 0.381 1.111 0.043 952 18307 SENSE 0.394 0.183 1.676 0.287 1.088 0.013 997 18352 SENSE 0.239 0.055 0.036 0.894 0.924 0.019 968 18421 SENSE 0.069 0.684 0.941 0.213 0.918 0.012 969 18422 SENSE 0.236 0.243 / / 1.127 0.033 958 18441 SENSE 0.175 0.289 0.832 0.497 0.907 0.043 979 18535 SENSE −0.007 0.946 −0.100 0.496 0.853 0.015 911 19041 ANTI- 0.160 0.012 −0.063 0.102 0.932 0.003 SENSE 913 19042 ANTI- 0.068 0.618 0.024 0.725 0.767 0.030 SENSE 950 19154 SENSE 0.109 0.609 1.642 0.111 0.877 0.041 951 19155 SENSE 0.244 0.237 0.085 0.434 0.905 0.018 976 19237 SENSE 0.094 0.296 0.492 0.362 0.663 0.047 971 19244 SENSE 0.473 0.104 1.137 0.259 1.324 0.020 1011 19320 SENSE −0.265 0.212 / / 0.329 0.043 967 19534 SENSE 0.064 0.756 0.920 0.315 0.630 0.039 964 19535 SENSE 0.190 0.158 −0.025 0.750 0.961 0.013 970 19539 SENSE 0.083 0.373 0.521 0.256 0.466 0.031 973 19545 SENSE −0.083 0.150 / / 0.609 0.038 1002 19616 SENSE 0.288 0.094 −0.068 0.565 0.689 0.003 1027 19702 SENSE −0.017 0.915 −0.033 0.798 0.783 0.043 1032 19755 SENSE 0.312 0.129 1.611 0.029 1.285 0.008 1029 19775 SENSE 0.126 0.362 2.093 0.172 0.775 0.004 1042 19786 SENSE 0.226 0.265 0.580 0.372 1.083 0.040 1039 19825 SENSE 0.053 0.662 −0.055 0.759 0.872 0.022 1037 19893 SENSE −0.089 0.168 −0.130 0.249 0.787 0.023 1040 19919 SENSE −0.214 0.277 0.198 0.435 0.814 0.050 1041 19979 SENSE 0.202 0.080 0.738 0.222 1.048 0.047 1031 19982 SENSE 0.241 0.111 0.933 0.263 1.127 0.025 1038 19983 SENSE 0.238 0.218 0.834 0.367 0.876 0.002 1028 19985 SENSE 0.216 0.057 0.414 0.306 0.860 0.001 1036 19987 SENSE 0.052 0.568 0.584 0.442 0.834 0.028 925 70102 SENSE −0.013 0.877 −0.115 0.461 0.779 0.012 926 70106 SENSE 0.038 0.667 −0.016 0.692 0.869 0.028 927 70113 SENSE 0.163 0.289 1.098 0.222 1.005 0.012 930 70128 SENSE 0.025 0.785 0.347 0.302 0.920 0.016 931 70130 SENSE 0.238 0.111 −0.041 0.447 1.275 0.000 884 70216 SENSE 0.012 0.932 0.165 0.689 0.708 0.007 1436 70229 SENSE −0.074 0.761 0.228 0.259 0.494 0.034 1446 70230 SENSE 0.068 0.053 −0.005 0.908 0.554 0.008 804 70244 SENSE 0.019 0.894 / / 0.468 0.036 845 70253 SENSE −0.080 0.196 −0.189 0.436 1.085 0.004 856 70412 SENSE 0.151 0.185 1.151 0.374 0.757 0.023 975 70425 SENSE −0.050 0.712 / / 0.815 0.011 1014 70433 SENSE 0.196 0.242 / / 0.737 0.021 1015 70434 SENSE 0.136 0.106 / / 0.814 0.000 1017 70436 SENSE 0.199 0.196 0.008 0.918 0.969 0.017 1019 70439 SENSE 0.188 0.127 0.846 0.311 1.250 0.012 1001 70603 SENSE 0.430 0.028 0.301 0.281 1.573 0.004 1052 70635 SENSE −0.199 0.020 −0.185 0.234 0.381 0.045 1054 70638 SENSE 0.004 0.943 −0.069 0.197 0.788 0.036 1055 70642 SENSE −0.100 0.336 −0.278 0.049 0.385 0.003 1056 70643 SENSE 0.160 0.445 −0.001 0.423 0.947 0.021 1078 70682 SENSE −0.203 0.156 −0.278 0.057 0.404 0.024 920 70706 ANTI- −0.354 0.066 −0.162 0.208 0.517 0.010 SENSE 843 70716 ANTI- 0.098 0.240 0.013 0.970 0.858 0.001 SENSE 837 70721 ANTI- 0.254 0.047 0.346 0.068 0.859 0.008 SENSE 859 70723 ANTI- 0.180 0.341 1.110 0.253 0.990 0.016 SENSE 1026 70741 SENSE 0.046 0.693 0.469 0.265 0.927 0.008 1093 70810 SENSE 0.168 0.053 −0.072 0.275 0.897 0.013 1008 70827 SENSE −0.106 0.519 0.878 0.158 0.646 0.045 880 70832 SENSE 0.224 0.152 1.398 0.318 0.912 0.008 1263 70850 SENSE −0.002 0.986 0.312 0.296 0.887 0.035 1043 70903 SENSE 0.065 0.734 0.623 0.454 0.776 0.002 1046 70936 SENSE 0.393 0.063 0.889 0.020 1.352 0.008 1044 70970 SENSE 0.335 0.231 0.520 0.444 1.429 0.031 1547 71107 SENSE −0.257 0.177 0.027 0.685 0.528 0.045 1126 71125 SENSE 0.236 0.091 1.197 0.112 1.308 0.029 921 71145 SENSE 0.093 0.534 / / 0.535 0.030 1604 71249 SENSE −0.150 0.372 0.056 0.768 0.866 0.035 977 71303 SENSE 0.103 0.377 / / 0.858 0.025 1067 71318 SENSE 0.100 0.212 0.498 0.324 1.190 0.004 957 71531 SENSE −0.087 0.696 −0.085 0.224 0.718 0.048 1006 71536 SENSE 0.021 0.831 −0.134 0.725 0.922 0.047 1057 71564 SENSE 0.305 0.153 0.033 0.795 0.793 0.013 1091 71629 SENSE 0.084 0.202 1.387 0.044 1.001 0.019 1083 71696 SENSE 0.222 0.304 0.850 0.296 0.885 0.043 965 71719 SENSE 0.113 0.605 0.088 0.689 0.989 0.046 1063 71808 SENSE 0.158 0.043 0.589 0.172 0.956 0.011 1143 72110 SENSE −0.031 0.607 −0.114 0.565 0.329 0.041 1142 72124 SENSE −0.211 0.255 −0.100 0.411 0.568 0.049 1542 72314 SENSE 0.127 0.271 1.270 0.224 0.943 0.002 1288 72340 SENSE 0.089 0.574 0.893 0.258 0.864 0.032 910 72427 ANTI- −0.024 0.813 −0.019 0.423 0.658 0.006 SENSE 1084 72475 SENSE −0.129 0.192 0.024 0.896 0.697 0.013 1087 72476 SENSE −0.136 0.228 −0.168 0.134 0.729 0.007 1098 72537 SENSE −0.124 0.341 −0.254 0.011 0.352 0.025 1169 72732 SENSE 0.191 0.165 0.090 0.641 0.700 0.020 933 72748 SENSE 0.125 0.369 1.403 0.138 1.010 0.000 1158 72749 SENSE 0.053 0.642 0.625 0.250 0.881 0.027 1161 72775 SENSE −0.050 0.707 −0.157 0.333 0.861 0.049 1163 72776 SENSE 0.091 0.358 1.128 0.239 1.244 0.006 1168 72791 SENSE −0.095 0.672 / / 0.763 0.034 1199 72909 SENSE 0.254 0.065 −0.033 0.348 0.818 0.048 1203 72958 SENSE −0.030 0.774 −0.052 0.358 0.840 0.034 1195 73018 SENSE 0.053 0.638 0.057 0.895 0.856 0.042 1202 73036 SENSE −0.005 0.957 0.282 0.386 0.783 0.007 1188 73074 SENSE −0.146 0.202 −0.081 0.319 0.667 0.028 1193 73077 SENSE 0.028 0.770 0.495 0.459 0.944 0.001 1196 73112 SENSE 0.021 0.846 / / 0.886 0.019 1180 73117 SENSE −0.060 0.537 0.124 0.759 0.996 0.018 1178 73128 SENSE 0.149 0.075 0.248 0.598 0.934 0.038 1191 73147 SENSE 0.689 0.024 0.822 0.293 1.572 0.010 1174 73174 SENSE 0.305 0.027 0.532 0.480 0.779 0.046 1194 73183 SENSE 0.113 0.617 0.180 0.573 0.969 0.004 1175 73186 SENSE 0.101 0.628 1.230 0.130 0.714 0.014 1131 73248 SENSE 0.289 0.103 0.455 0.104 1.034 0.018 1118 73353 SENSE 0.108 0.504 0.947 0.218 0.864 0.024 1264 73429 SENSE 0.305 0.067 0.867 0.057 1.190 0.003 1267 73455 SENSE 0.133 0.064 0.299 0.033 0.559 0.018 1262 73474 SENSE −0.433 0.105 −0.164 0.092 0.433 0.024 1274 73538 SENSE −0.003 0.962 0.241 0.339 0.741 0.003 1279 73565 SENSE 0.182 0.325 0.650 0.525 1.279 0.021 1275 73574 SENSE 0.067 0.721 0.363 0.636 0.758 0.043 996 73607 SENSE −0.070 0.388 0.401 0.673 0.636 0.024 896 73706 SENSE 0.064 0.744 0.294 0.124 1.082 0.012 1144 73916 SENSE −0.004 0.980 0.495 0.265 1.060 0.024 903 73977 SENSE 0.230 0.065 0.096 0.370 0.596 0.014 1182 73990 SENSE 0.133 0.346 / / 1.140 0.025 1291 74133 SENSE −0.170 0.121 −0.027 0.729 0.635 0.013 1289 74155 SENSE 0.211 0.210 0.458 0.420 0.945 0.017 1148 74273 SENSE 0.050 0.756 0.694 0.467 0.837 0.026 1149 74280 SENSE 0.117 0.251 −0.103 0.271 0.785 0.002 1151 74287 SENSE 0.044 0.644 −0.148 0.027 0.928 0.000 1206 74333 SENSE 0.144 0.114 0.144 0.521 0.748 0.023 1299 74431 SENSE 0.002 0.987 −0.190 0.282 0.674 0.012 1293 74485 SENSE −0.007 0.920 −0.098 0.273 0.923 0.007 1435 74508 SENSE 0.409 0.104 0.221 0.394 0.825 0.001 1302 74525 SENSE 0.110 0.261 0.080 0.467 0.967 0.004 1227 74612 SENSE −0.319 0.220 −0.591 0.063 0.563 0.017 1233 74623 SENSE −0.167 0.140 / / 0.521 0.000 1237 74638 SENSE 0.036 0.848 0.418 0.399 0.828 0.049 1209 74737 SENSE 0.004 0.959 0.877 0.414 0.972 0.008 1212 74747 SENSE 0.254 0.074 1.728 0.157 0.961 0.027 1355 74804 SENSE 0.615 0.095 1.179 0.314 1.685 0.019 1352 74826 SENSE −0.062 0.460 / / 0.655 0.009 1353 74850 SENSE 0.167 0.271 0.910 0.352 0.950 0.040 1359 74901 SENSE 0.117 0.664 0.258 0.353 0.897 0.041 1361 74904 SENSE −0.030 0.814 −0.030 0.791 0.866 0.016 1365 74966 SENSE −0.041 0.658 0.114 0.770 0.671 0.015 1360 74974 SENSE 0.142 0.382 −0.117 0.116 0.793 0.047 1130 75206 SENSE 0.044 0.484 −0.217 0.093 0.671 0.010 1254 75281 SENSE 0.207 0.020 0.046 0.795 0.827 0.009 1380 75323 SENSE 0.041 0.684 −0.202 0.074 0.473 0.006 1374 75330 SENSE −0.005 0.712 −0.001 0.998 0.753 0.001 1379 75334 SENSE 0.427 0.107 0.050 0.599 1.040 0.004 1376 75366 SENSE −0.013 0.883 / / 0.832 0.008 1372 75389 SENSE 0.304 0.038 0.181 0.377 0.923 0.005 1378 75391 SENSE 0.076 0.434 0.109 0.434 0.918 0.020 1382 75401 SENSE 0.020 0.910 / / 0.854 0.005 1392 75446 SENSE 0.431 0.174 0.231 0.269 0.967 0.021 1390 75454 SENSE 0.055 0.585 0.288 0.378 0.770 0.022 1384 75461 SENSE 0.032 0.434 0.020 0.936 0.931 0.034 1388 75464 SENSE −0.117 0.288 0.085 0.651 0.717 0.014 1391 75493 SENSE 0.007 0.891 −0.021 0.738 1.080 0.013 1401 75512 SENSE 0.089 0.652 0.860 0.279 0.806 0.032 1409 75605 SENSE 0.153 0.136 −0.016 0.721 1.065 0.014 1413 75623 SENSE 0.151 0.321 −0.030 0.721 0.751 0.000 1403 75626 SENSE 0.364 0.001 0.619 0.475 1.127 0.014 1404 75674 SENSE −0.028 0.530 / / 0.893 0.021 1415 75695 SENSE 0.132 0.300 0.072 0.640 1.108 0.010 1419 75714 SENSE −0.049 0.701 0.169 0.588 0.853 0.025 1308 75832 SENSE 0.043 0.229 −0.006 0.944 0.691 0.013 1318 75848 SENSE 0.117 0.485 0.324 0.491 0.953 0.035 1321 75852 SENSE −0.218 0.196 −0.017 0.895 0.468 0.039 1330 75879 SENSE 0.126 0.570 −0.007 0.937 0.863 0.042 1331 75880 SENSE 0.198 0.119 0.331 0.249 0.842 0.011 1468 75908 SENSE 0.057 0.686 −0.064 0.759 0.916 0.015 1467 75919 SENSE −0.063 0.562 −0.056 0.586 0.640 0.036 1471 75933 SENSE 0.126 0.099 0.431 0.238 0.905 0.004 1466 75940 SENSE 0.147 0.429 1.316 0.343 0.872 0.049 830 75958 SENSE 0.036 0.515 −0.144 0.102 1.048 0.001 826 75969 SENSE 0.164 0.316 0.002 0.990 0.696 0.025 1470 75992 SENSE 0.103 0.525 0.101 0.605 0.853 0.005 832 76002 SENSE −0.016 0.860 0.032 0.815 0.868 0.023 892 76017 SENSE 0.107 0.424 0.359 0.280 0.978 0.022 843 76039 SENSE 0.226 0.299 0.039 0.656 1.072 0.008 914 76053 SENSE 0.293 0.058 0.940 0.022 1.142 0.004 1215 76212 SENSE 0.006 0.732 0.105 0.829 0.808 0.012 1258 76236 SENSE −0.062 0.693 0.941 0.453 0.871 0.031 1314 76261 SENSE 0.065 0.490 0.699 0.344 0.901 0.039 1526 76337 SENSE 0.121 0.439 0.454 0.199 0.924 0.010 1532 76378 SENSE −0.077 0.500 0.220 0.481 0.829 0.034 1536 76381 SENSE −0.011 0.954 0.712 0.324 0.806 0.004 1340 76462 SENSE −0.019 0.861 −0.004 0.959 0.716 0.038 1221 76530 SENSE 0.260 0.305 −0.053 0.801 1.088 0.004 1342 76568 SENSE −0.008 0.748 0.059 0.677 0.610 0.016 1337 76621 SENSE −0.098 0.270 0.001 0.995 0.622 0.006 1346 76629 SENSE 0.154 0.603 0.550 0.509 0.982 0.049 1222 76716 SENSE −0.007 0.945 / / 0.792 0.024 1333 76745 SENSE 0.044 0.738 −0.010 0.927 0.695 0.021 1550 76805 SENSE 0.369 0.113 0.041 0.519 0.950 0.018 1551 76817 SENSE 0.126 0.645 0.007 0.790 0.861 0.024 1562 76848 SENSE −0.080 0.699 −0.112 0.185 0.804 0.006 1558 76869 SENSE 0.345 0.160 1.378 0.130 1.205 0.030 1548 76887 SENSE 0.319 0.292 / / 0.812 0.036 1554 76890 SENSE 0.226 0.007 −0.032 0.300 0.659 0.027 1567 76904 SENSE 0.178 0.268 / / 0.917 0.004 1310 77034 SENSE −0.033 0.843 0.479 0.109 0.953 0.001 1572 77127 SENSE 0.061 0.705 −0.026 0.704 0.769 0.043 1582 77171 SENSE 0.054 0.519 −0.133 0.026 0.698 0.000 1575 77179 SENSE 0.146 0.392 0.039 0.517 1.072 0.010 1587 77184 SENSE 0.025 0.782 / / 0.979 0.012 1153 77304 SENSE 0.174 0.297 1.437 0.321 1.010 0.047 1223 77328 SENSE 0.116 0.253 / / 1.016 0.024 1445 77345 SENSE 0.222 0.005 0.215 0.529 0.833 0.010 1447 77353 SENSE 0.124 0.184 0.043 0.702 0.830 0.007 1594 77414 SENSE 0.115 0.229 / / 0.965 0.002 1601 77419 SENSE 0.309 0.205 0.762 0.199 1.166 0.013 1600 77442 SENSE 0.112 0.214 0.779 0.067 0.825 0.019 1596 77463 SENSE −0.027 0.865 −0.143 0.007 0.674 0.045 1319 77515 SENSE 0.242 0.195 0.088 0.276 1.411 0.014 1332 77519 SENSE 0.667 0.043 1.824 0.173 1.142 0.021 1323 77523 SENSE 0.190 0.379 1.044 0.059 1.312 0.014 1426 77554 SENSE 0.358 0.257 1.126 0.108 0.949 0.034 1430 77560 SENSE −0.047 0.095 0.786 0.380 0.583 0.012 1438 77567 SENSE −0.178 0.220 / / 0.437 0.020 1440 77578 SENSE 0.213 0.119 1.089 0.387 0.931 0.013 1270 77726 SENSE −0.060 0.338 / / 0.990 0.007 1368 77814 SENSE −0.032 0.843 −0.117 0.556 0.885 0.025 1395 77818 SENSE 0.094 0.220 0.336 0.311 0.879 0.004 1248 77903 SENSE 0.014 0.798 0.015 0.874 0.675 0.017 1443 77925 SENSE 0.005 0.960 0.085 0.472 0.911 0.001 1444 77927 SENSE −0.167 0.181 −0.114 0.590 0.638 0.002 1456 77937 SENSE 0.231 0.151 0.815 0.062 1.368 0.001 1458 77940 SENSE −0.017 0.859 / / 0.706 0.004 1421 77954 SENSE 0.326 0.111 1.981 0.208 1.139 0.014 1422 77955 SENSE −0.078 0.652 −0.062 0.104 0.529 0.029 1437 77959 SENSE 0.345 0.055 0.505 0.429 1.016 0.038 1474 77972 SENSE 0.101 0.481 0.125 0.606 1.030 0.008 1495 78019 SENSE 0.030 0.321 0.320 0.481 0.931 0.034 1429 78128 SENSE 0.341 0.052 0.016 0.764 1.007 0.021 1424 78131 SENSE 0.042 0.138 0.018 0.829 0.687 0.005 1499 78161 SENSE 0.156 0.202 0.170 0.418 0.898 0.000 1522 78191 SENSE 0.177 0.313 0.964 0.512 0.854 0.020 1061 78321 SENSE 0.196 0.245 −0.007 0.773 1.013 0.048 1110 78325 SENSE 0.046 0.345 0.123 0.609 0.643 0.007 1232 78364 SENSE 0.054 0.615 0.837 0.243 0.475 0.038 1239 78365 SENSE 0.083 0.384 / / 1.153 0.030 948 78370 SENSE 0.016 0.854 0.310 0.456 0.826 0.036 1000 78373 SENSE 0.018 0.774 0.595 0.263 1.046 0.009 1482 78538 SENSE 0.123 0.332 1.152 0.342 0.921 0.024 1490 78543 SENSE −0.003 0.979 / / 0.934 0.008 1513 78566 SENSE 0.131 0.429 0.479 0.532 0.820 0.017 1523 78595 SENSE 0.182 0.295 0.005 0.938 0.766 0.014 1520 78632 SENSE 0.394 0.058 0.997 0.314 1.143 0.017 1459 78746 SENSE 0.192 0.256 1.115 0.346 1.025 0.013 1455 78904 SENSE 0.150 0.222 0.970 0.084 0.946 0.030 1483 78922 SENSE 0.162 0.307 2.327 0.024 1.156 0.007 1341 78987 SENSE −0.034 0.626 0.689 0.246 0.828 0.005 1434 78994 SENSE 0.282 0.000 2.384 0.009 0.940 0.002

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 823, 825, 873, 886, 912, 916, 919, 928, 937, 942, 972, 986, 995, 1074, 1107, 1134, 1136, 1145, 1157, 1173, 1220, 1228, 1242, 1243, 1285, 1377,1469, 1486, 1489, 1524, 1538, 1546, 1556, 1568, 1571, 1574, 1592, or 1603 showed enhanced heat stress tolerance by the second criteria as illustrated in Example 1L and 1M.

D. Salt Stress Tolerance Screen

This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.

T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the experiment were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m². On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve high salinity tolerance in transgenic plants illustrated in Table 6.

TABLE 6 Root length at day 11 Root length at day 14 Growth stage at day 14 Seedling weight at day 14 PEP Delta Delta Delta Delta SEQ ID Orientation mean P-value mean P-value mean P-value mean P-value 932 ANTI-SENSE 0.305 0.019 0.360 0.093 0.583 0.428 0.835 0.050 955 SENSE 0.028 0.336 0.085 0.047 −0.038 0.866 0.060 0.036 1093 SENSE 0.097 0.010 0.046 0.488 0.605 0.172 0.166 0.016 1139 SENSE 0.187 0.011 0.092 0.015 −0.038 0.923 −0.002 0.987 1183 SENSE 0.251 0.118 0.328 0.016 / / 0.404 0.148 1106 SENSE 0.093 0.383 0.169 0.030 0.370 0.357 0.215 0.053 896 SENSE 0.349 0.000 0.270 0.069 0.057 0.797 0.421 0.047 1416 SENSE 0.062 0.516 0.081 0.035 −0.159 0.513 −0.076 0.670 1591 SENSE 0.034 0.592 0.051 0.003 0.255 0.623 0.194 0.052 1598 SENSE 0.227 0.004 0.224 0.002 1.203 0.316 0.281 0.258 1425 SENSE −0.107 0.327 −0.028 0.724 −0.215 0.425 0.384 0.029 1384 SENSE −0.088 0.195 −0.0557 0.531 −0.009 0.980 0.101 0.025

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 821, 834, 890, 919, 946, 961, 997, 1013, 1080, 1101, 1147, 1160, 1181, 1197, 1200, 1220, 1237, 1248, 1264, 1300, 1313, 1355, 1393, 1397, 1406, 1467, 1496, 1514, 1530 or 1561 showed enhanced salt stress tolerance by the second criteria as illustrated in Example 1L and 1M.

E. Polyethylene Glycol (PEG) Induced Osmotic Stress Tolerance Screen

There are numerous factors, which can influence seed germination and subsequent seedling growth, one being the availability of water. Genes, which can directly affect the success rate of germination and early seedling growth, are usable agronomic traits for improving the germination and growth of crop plants under drought stress. In this assay, PEG was used to induce osmotic stress on germinating transgenic lines of Arabidopsis thaliana seeds in order to screen for osmotically resistant seed lines.

T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, ½× MS salts, 1% phytagel, and 10 μg/ml glufosinate. Plates placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, e.g., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14.

Seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm. The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants illustrated in Table 7.

TABLE 7 Root length at day 11 Root length at day 14 Growth stage at day 14 Seedling weight at day 14 PEP Delta Delta Delta Delta Seq ID Orientation mean P-value mean P-value mean P-value mean P-value 1019 SENSE 0.003 0.883 0.068 0.022 0.113 0.715 −0.139 0.215 960 SENSE 0.139 0.278 0.065 0.010 2.264 0.322 0.197 0.256 1241 SENSE 0.061 0.690 0.096 0.044 1.011 0.569 −0.095 0.666 1119 SENSE 0.002 0.978 −0.107 0.415 2.760 0.156 0.156 0.000 1391 SENSE 0.602 0.012 0.533 0.044 / / 0.866 0.005 1322 SENSE 0.062 0.041 0.150 0.020 / / −0.132 0.218 1238 SENSE 0.099 0.387 0.118 0.004 2.693 0.175 −0.187 0.005 1556 SENSE 0.153 0.116 0.271 0.081 / / 0.331 0.019 1153 SENSE 0.063 0.067 0.081 0.134 2.964 0.104 0.280 0.020 1218 SENSE 0.040 0.067 −0.089 0.170 0.492 0.806 0.198 0.030 1599 SENSE 0.099 0.168 0.103 0.237 / / 0.292 0.031 1478 SENSE 0.216 0.115 0.197 0.041 1.353 0.414 0.234 0.388 1512 SENSE −0.167 0.071 −0.230 0.141 −1.066  0.090 0.085 0.012 1572 SENSE 0.447 0.005 0.352 0.025 4    / 0.656 0.046

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 832, 833, 871, 874, 931, 974, 985, 997, 1021, 1024, 1031, 1043, 1053, 1059, 1060, 1091, 1111, 1115, 1118, 1120, 1124, 1127, 1128, 1159, 1172, 1179, 1185, 1197, 1213, 1226, 1230, 1244, 1253, 1265, 1306, 1320, 1327, 1354, 1355, 1357, 1362, 1367, 1381, 1395, 1398, 1399, 1407, 1462, 1494, 1499, 1500, 1523, 1529, 1532, 1544, 1548, 1569, 1572, 1573, 1595, or 1598 showed enhanced PEG osmotic stress tolerance by the second criteria as illustrated in Example 1L and 1M.

F. Cold Shock Tolerance Screen

This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.

Eleven seedlings from T2 seeds of each transgenic line plus one control line were plated together on a plate containing ½× Gamborg Salts with 0.8 Phytagel™, 1% Phytagel, and 0.3% Sucrose. Plates were then oriented horizontally and stratified for three days at 4° C. At day three, plates were removed from stratification and exposed to standard conditions (16 hr photoperiod, 22° C. at day and 20° C. at night) until day 8. At day eight, plates were removed from standard conditions and exposed to cold shock conditions (24 hr photoperiod, 8° C. at both day and night) until the final day of the assay, e.g., day 28. Rosette areas were measured at day 8 and day 28, which were analyzed as quantitative responses according to example 1M. A list of recombinant nucleotides that improve cold shock stress tolerance in plants illustrated in Table 8.

TABLE 8 Rosette area Rosette area at day 28 Rosette area PEP Con- at day 8 Risk difference SEQ struct Orien- Delta P- score P- Delta P- ID ID tation mean value mean value mean value 814 72361 SENSE 0.172 0.712 0.657 0.000 0.757 0.001 816 71626 SENSE 0.634 0.013 0.456 0.032 0.513 0.003 861 13965 ANTI- 0.414 0.077 0.248 0.117 0.274 0.012 SENSE 915 16120 SENSE 0.494 0.247 0.758 0.042 0.722 0.077 918 72417 SENSE 0.984 0.041 0.125 0.023 0.114 0.051 923 71706 SENSE 0.010 0.943 0.231 0.064 0.459 0.019 962 70808 SENSE 0.394 0.285 0.290 0.014 0.362 0.072 974 72356 SENSE 0.570 0.057 0.823 0.044 0.888 0.096 1000 78373 SENSE −0.020 0.948 0.846 0.006 0.923 0.005 1012 73613 SENSE 0.574 0.024 0.579 0.010 0.570 0.012 1022 70447 SENSE 0.294 0.369 0.195 0.015 0.106 0.089 1023 71725 SENSE 0.201 0.492 0.199 0.026 0.225 0.055 1085 71677 SENSE 0.596 0.003 0.741 0.021 0.425 0.226 1097 72510 SENSE 0.813 0.250 0.891 0.009 1.105 0.015 1125 73221 SENSE 0.582 0.016 0.412 0.027 0.425 0.117 1141 72092 SENSE 0.092 0.750 0.568 0.006 0.480 0.027 1151 74287 SENSE 0.692 0.065 0.795 0.017 0.774 0.015 1153 77304 SENSE 0.664 0.194 1.164 0.014 1.479 0.014 1156 74719 SENSE 0.350 0.133 0.393 0.083 0.449 0.013 1171 73058 SENSE 0.500 0.180 0.322 0.027 0.329 0.049 1186 73131 SENSE 0.369 0.286 0.725 0.031 0.907 0.052 1187 73108 SENSE 0.579 0.065 0.725 0.018 0.644 0.025 1198 10908 ANTI- −0.549 0.086 0.112 0.095 0.136 0.050 SENSE 1205 74732 SENSE 0.348 0.082 0.457 0.059 0.513 0.019 1239 78365 SENSE 0.430 0.141 0.621 0.035 0.600 0.043 1307 75830 SENSE 0.865 0.113 1.430 0.003 1.558 0.002 1315 78456 SENSE −0.352 0.118 0.534 0.077 0.650 0.049 1335 76746 SENSE 0.552 0.112 0.508 0.071 0.734 0.041 1343 76176 SENSE 0.435 0.095 1.337 0.018 1.472 0.018 1350 78115 SENSE 0.136 0.464 0.413 0.016 0.421 0.018 1375 75342 SENSE 1.019 0.029 1.486 0.039 1.752 0.046 1408 75652 SENSE −0.425 0.454 0.388 0.005 0.415 0.009 1409 75605 SENSE 0.424 0.100 0.703 0.041 0.808 0.010 1420 75762 SENSE 1.078 0.039 0.558 0.037 0.480 0.011 1430 77560 SENSE 0.378 0.128 0.261 0.028 0.288 0.041 1431 77561 SENSE −0.191 0.296 0.446 0.054 0.511 0.047 1439 11749 ANTI- −0.458 0.494 0.622 0.028 0.710 0.008 SENSE 1458 77940 SENSE 0.498 0.200 0.305 0.167 0.573 0.009 1461 78126 SENSE −0.708 0.080 0.426 0.046 0.485 0.071 1500 78162 SENSE 1.502 0.000 1.496 0.025 1.778 0.024 1502 78622 SENSE 0.550 0.221 0.722 0.018 0.752 0.016 1517 78571 SENSE 1.529 0.033 1.204 0.001 1.303 0.001 1519 78573 SENSE 0.292 0.457 0.603 0.007 0.542 0.038 1543 77840 SENSE −0.182 0.173 0.232 0.030 0.299 0.020 1565 76939 SENSE 0.598 0.154 0.520 0.037 0.597 0.035 1566 76987 SENSE 0.953 0.052 0.845 0.010 0.936 0.007 1577 77145 SENSE 0.408 0.180 0.403 0.041 0.368 0.140 1593 77462 SENSE 1.157 0.052 1.077 0.012 0.969 0.003 1601 77419 SENSE 0.156 0.513 0.763 0.010 0.844 0.031 1605 71237 SENSE 0.836 0.009 0.825 0.005 1.041 0.007 845 70253 SENSE 0.578 0.007 0.571 0.064 0.459 0.007 1007 70419 SENSE −0.079 0.646 0.197 0.126 0.266 0.012 1313 77511 SENSE 0.822 0.011 0.131 0.013 0.063 0.189 1332 77519 SENSE 0.275 0.286 0.911 0.034 1.020 0.031 1484 77984 SENSE −0.104 0.724 0.255 0.055 0.274 0.048 Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 818, 836, 844, 848, 883, 1029, 1045, 1062, 1082, 1277, 1287, 1294, 1305, 1318, 1366, 1369, 1373, 1387, 1402, 1405, 1410, 1412, 1418, 1427, 1433, 1476, 1481, 1495, 1531, or 1583 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.

G. Cold Germination Tolerance Screen

This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.

T2 seeds were plated and all seedlings used in the experiment were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of ½× Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% Phytagel™ (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plate were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m²/s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.

The root length at day 28 was analyzed as a quantitative response according to example 1M. The growth stage at day 7 was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve cold stress tolerance in transgenic plants illustrated in Table 9.

TABLE 9 Root length at day 28 Growth stage at day 28 NUC PEP Construct Nomination Delta Delta Seq ID NO SEQ ID NO ID ID Orientation mean P-value mean P-value 187 990 18331 CGPG3338 SENSE / / / / 227 1030 19829 CGPG3981 SENSE −0.021 0.389 0.597 0.031 231 1034 70365 CGPG4028 SENSE −0.088 0.312 0.725 0.013 214 1017 70436 CGPG3703 SENSE 0.051 0.747 1.952 0.005 217 1020 70446 CGPG3730 SENSE −0.064 0.784 1.572 0.009 159 962 70808 CGPG289 SENSE 0.090 0.637 2.318 0.003 262 1065 71313 CGPG4401 SENSE 0.160 0.542 1.654 0.001 272 1075 71339 CGPG4551 SENSE / / / / 283 1086 71691 CGPG4656 SENSE −0.048 0.305 1.121 0.003 335 1138 72016 CGPG5246 SENSE 0.385 0.012 1.855 0.161 337 1140 72044 CGPG5268 SENSE 0.442 0.044 1.908 0.003 359 1162 72728 CGPG5530 SENSE 0.243 0.300 2.142 0.002 137 940 72796 CGPG2451 SENSE 0.187 0.063 0.775 0.014 92 895 72952 CGPG2095 SENSE / / / / 399 1202 73036 CGPG5796 SENSE 0.246 0.127 2.235 0.001 64 867 73075 CGPG1797 SENSE 0.046 0.788 1.242 0.007 377 1180 73117 CGPG5657 SENSE 0.384 0.033 1.764 0.001 386 1189 73132 CGPG5705 SENSE 0.208 0.283 2.646 0.003 374 1177 73139 CGPG5641 SENSE 0.040 0.536 1.183 0.002 473 1276 73539 CGPG6475 SENSE 0.004 0.967 1.052 0.002 482 1285 74104 CGPG6566 SENSE 0.107 0.490 1.060 0.003 428 1231 74381 CGPG6111 SENSE 0.060 0.631 0.457 0.049 632 1435 74508 CGPG8 SENSE 0.323 0.009 1.197 0.387 433 1236 74635 CGPG6147 SENSE 0.165 0.172 1.596 0.006 438 1241 74660 CGPG6177 SENSE 0.358 0.007 1.518 0.001 571 1374 75330 CGPG7508 SENSE 0.019 0.906 0.570 0.026 589 1392 75446 CGPG7637 SENSE / / / / 598 1401 75512 CGPG7752 SENSE 0.057 0.576 1.652 0.001 595 1398 75582 CGPG7742 SENSE 0.213 0.374 1.883 0.003 506 1309 75836 CGPG6827 SENSE 0.228 0.076 1.314 0.041 521 1324 75863 CGPG6942 SENSE 0.162 0.132 1.468 0.002 523 1326 75865 CGPG6949 SENSE 0.046 0.615 1.742 0.006 660 1463 75901 CGPG8211 SENSE 0.437 0.015 1.733 0.070 59 862 75912 CGPG1726 SENSE −0.035 0.550 0.265 0.000 37 840 76050 CGPG1463 SENSE −0.146 0.404 0.213 0.043 408 1211 76113 CGPG5862 SENSE 0.135 0.014 0.615 0.453 544 1347 76189 CGPG7253 SENSE 0.015 0.018 0.333 0.645 722 1525 76325 CGPG8870 SENSE −0.141 0.553 0.557 0.026 447 1250 76524 CGPG6266 SENSE 0.099 0.300 1.123 0.015 446 1249 76653 CGPG6254 SENSE 0.507 0.101 3.257 0.004 628 1431 77561 CGPG7972 SENSE 0.278 0.061 1.265 0.009 647 1450 77588 CGPG8108 SENSE 0.063 0.677 1.028 0.032 749 1552 77843 CGPG9017 SENSE 0.382 0.011 1.325 0.006 701 1504 78043 CGPG8606 SENSE 0.237 0.204 0.859 0.003 91 894 17227 CGPG2077 SENSE 0.071 0.621 0.820 0.006 319 1122 73318 CGPG5029 SENSE 0.004 0.989 0.532 0.011 465 1268 73432 CGPG6421 SENSE −0.038 0.743 0.532 0.011 568 1371 77808 CGPG7499 SENSE 0.170 0.037 1.138 0.023 312 1115 72814 CGPG4982 SENSE 0.080 0.592 1.467 0.013 461 1264 73429 CGPG6397 SENSE 0.320 0.206 1.589 0.017 682 1485 73938 CGPG85 SENSE 0.029 0.927 1.140 0.005 680 1483 78922 CGPG8489 SENSE 0.260 0.123 1.326 0.004

Transgenic plants comprising recombinant DNA expressing protein as set forth in 826, 863, 864, 941, 985, 1071, 1123, 1170, 1194, 1259, 1312, 1339, 1433, 1465, 1543, 1556 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.

H. Shade Tolerance Screen

Plants undergo a characteristic morphological response in shade that includes the elongation of the petiole, a change in the leaf angle, and a reduction in chlorophyll content. While these changes can confer a competitive advantage to individuals, in a monoculture the shade avoidance response is thought to reduce the overall biomass of the population. Thus, genetic alterations that prevent the shade avoidance response can be associated with higher yields. Genes that favor growth under low light conditions can also promote yield, as inadequate light levels frequently limit yield. This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.

T2 seeds were plated on glufosinate selection plates with ½ MS medium. Seeds were sown on ½× MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m²/s, far/red ratio (655/665/725/735) ˜0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.

A list of recombinant DNA constructs that improve shade tolerance in plants illustrated in Table 10.

TABLE 10 Seedling weight Petiole length NUC PEP Con- at day 23 at day 23 Seq SEQ struct Orien- Delta P- Delta P- ID ID ID tation mean value mean value 52 855 15624 SENSE 0.327 0.041 0.141 0.189 398 1201 72922 SENSE 0.421 0.049 0.339 0.070 427 1230 74377 SENSE 0.411 0.039 0.374 0.067 405 1208 74736 SENSE 0.268 0.024 0.147 0.141 566 1369 75387 SENSE 0.329 0.008 0.342 0.010 59 862 75912 SENSE 0.470 0.035 0.572 0.058 664 1467 75919 SENSE 0.453 0.007 0.114 0.063 736 1539 76335 SENSE −1.012 0.081 −0.594 0.007 783 1586 77172 SENSE 0.426 0.044 0.218 0.164 698 1501 78033 SENSE 0.060 0.033 −0.129 0.612

For “seeding weight”, if p<0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p<0.2.

For “petiole length”, if p<0.05 and delta <0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta <0, the transgenic plants showed a trend of trait enhancement as compared to the reference.

Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 805, 828, 833, 870, 936, 937, 939, 965, 988, 1007, 1010, 1016, 1038, 1050, 1060, 1070, 1079, 1089, 1095, 1100, 1117, 1125, 1129, 1134, 1135, 1145,1150, 1154, 1155, 1158, 1184, 1204, 1210, 1214, 1216, 1217, 1225, 1226, 1235, 1248, 1252, 1255, 1260, 1271, 1278, 1282, 1283, 1289, 1292, 1297, 1304, 1311, 1312, 1317, 1328, 1336, 1338, 1348, 1363, 1366, 1383, 1386, 1400, 1428, 1448, 1451, 1453, 1462, 1491, 1493, 1505, 1516, 1520, 1528, 1533, 1545, 1579, or 1588 showed enhanced tolerance to shade or low light condition by the second criteria as illustrated in Example 1L and 1M.

I. Early Plant Growth and Development Screen

This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth. In this screen, we were looking for genes that confer advantages in the processes of germination, seedling vigor, root growth and root morphology under non-stressed growth conditions to plants. The transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.

T2 seeds were plated on glufosinate selection plates and grown under standard conditions (˜100 uE/m²/s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.

A list recombinant DNA constructs that improve early'plant growth and development illustrated in Table 11.

TABLE 11 Seedling Root length Root length weight NUC PEP at day 10 at day 14 at day 14 SEQ SEQ Orien- Delta P- Delta P- Delta P- ID ID tation mean value mean value mean value 52 855 SENSE 0.091 0.027 0.071 0.018 0.037 0.744 102 905 SENSE 0.188 0.210 0.104 0.247 0.308 0.021 121 924 SENSE 0.242 0.015 0.128 0.063 0.203 0.078 153 956 SENSE 0.153 0.027 0.122 0.197 0.256 0.010 134 937 SENSE 0.329 0.048 0.250 0.085 0.712 0.020 144 947 SENSE 0.127 0.146 0.045 0.566 0.371 0.023 101 904 SENSE 0.537 0.026 0.356 0.004 0.634 0.021 178 981 SENSE 0.372 0.136 0.273 0.033 0.346 0.082 179 982 SENSE 0.404 0.001 0.222 0.051 0.288 0.111 191 994 SENSE 0.282 0.008 0.285 0.009 0.445 0.012 163 966 SENSE 0.132 0.219 0.121 0.035 0.135 0.439 74 877 SENSE 0.282 0.033 0.166 0.015 0.143 0.363 162 965 SENSE 0.320 0.119 0.253 0.035 0.458 0.109 296 1099 SENSE 0.047 0.653 0.057 0.369 0.141 0.013 313 1116 SENSE 0.222 0.124 0.166 0.039 0.187 0.202 400 1203 SENSE 0.103 0.336 0.171 0.067 0.263 0.049 459 1262 SENSE 0.278 0.081 0.273 0.027 0.308 0.121 215 1018 SENSE 0.138 0.023 0.088 0.068 0.167 0.092 498 1301 SENSE 0.248 0.245 0.203 0.100 0.435 0.002 492 1295 SENSE 0.066 0.018 −0.052 0.334 0.215 0.171 567 1370 SENSE −0.134 0.218 0.030 0.770 −0.132 0.305 611 1414 SENSE 0.232 0.220 0.168 0.035 0.165 0.319 614 1417 SENSE 0.142 0.277 0.147 0.174 0.167 0.562 616 1419 SENSE 0.038 0.549 0.046 0.130 −0.028 0.873 526 1329 SENSE −0.044 0.135 0.070 0.044 −0.026 0.085 663 1466 SENSE 0.075 0.043 −0.065 0.418 0.047 0.639 79 882 SENSE 0.127 0.094 0.117 0.041 0.111 0.266 724 1527 SENSE 0.512 0.024 0.437 0.010 0.634 0.001 737 1540 SENSE −0.011 0.931 0.120 0.151 −0.090 0.487 248 1051 SENSE 0.197 0.003 0.145 0.007 0.020 0.783 444 1247 SENSE 0.369 0.009 0.279 0.012 0.255 0.004 741 1544 SENSE 0.205 0.011 0.129 0.350 0.168 0.158 522 1325 SENSE 0.134 0.354 0.160 0.069 0.085 0.653 777 1580 SENSE 0.218 0.022 0.064 0.601 0.067 0.770 775 1578 SENSE −0.192 0.322 0.019 0.780 −0.333 0.091 629 1432 SENSE −0.042 0.151 0.075 0.016 −0.184 0.176 704 1507 SENSE −0.074 0.546 0.123 0.058 0.113 0.433 697 1500 SENSE 0.173 0.049 0.078 0.546 0.109 0.054 706 1509 SENSE 0.074 0.018 0.076 0.301 0.059 0.664 331 1134 SENSE 0.107 0.013 0.050 0.569 0.202 0.178 546 1349 SENSE −0.182 0.037 −0.050 0.104 −0.150 0.613 717 1520 SENSE 0.297 0.085 0.223 0.029 0.292 0.213 22 825 SENSE / / / / 0.444 0.025 581 1384 SENSE 0.116 0.126 0.193 0.013 0.181 0.175 726 1529 SENSE 0.375 0.012 0.088 0.188 0.353 0.015 755 1558 SENSE 0.409 0.031 0.203 0.091 0.346 0.198

Transgenic plants comprising recombinant DNA expressing a protein as set forth in 810, 831, 844, 857, 865, 884, 892, 917, 950, 954, 970, 983, 992, 998, 1004, 1005, 1029, 1033, 1043, 1072, 1101, 1109, 1115, 1133, 1181, 1200, 1284, 1310, 1340, 1384, 1391, 1443, 1449, 1471, 1480, 1483, 1498, 1506, 1508, 1510, 1529, 1548, 1553, 1555, 1556, 1558, 1559, 1564, 1576, or 1577 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.

J. Late Plant Growth and Development Screen

This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.

Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft³. T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ˜5 per 2½″ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat. Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ˜200 μmoles/m²/s. Day and night temperature, set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.

Application of the herbicide glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ˜3 days after the selection was applied.

The rosette radius was measured at day 25. The silique length was measured at day 40. The plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53. The seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M. A list of recombinant DNA constructs that improve late plant growth and development illustrated in Table 12.

TABLE 12 Rosette dry weight at Rosette radius at Seed net dry weight at Silique dry weight at Silique length at day 53 day 25 day 62 day 53 day 40 PEP Construct Delta Delta Delta Delta Delta SEQ ID ID mean P-value mean P-value mean P-value mean P-value mean P-value 835 14405 0.110 0.430 / / 0.557 0.001 0.200 0.214 0.043 0.252 869 14833 0.247 0.382 / / 1.126 0.021 0.587 0.044 0.075 0.340 887 15207 0.238 0.023 −0.407 0.087 0.047 0.785 0.343 0.046 −0.015 0.540 949 70411 0.181 0.008 / / −0.268 0.192 0.061 0.025 −0.039 0.240 1057 71564 0.397 0.049 0.190 0.205 0.440 0.005 0.342 0.035 0.070 0.043 1066 72349 0.174 0.011 / / −0.526 0.049 −0.292 0.131 0.041 0.265 1102 72630 0.200 0.022 / / 0.537 0.030 −0.257 0.034 −0.297 0.015 1108 73347 0.063 0.559 −0.046 0.475 0.848 0.035 0.243 0.188 −0.005 0.706 944 16612 −0.438 0.116 −0.280 0.026 0.493 0.023 −0.746 0.034 −0.023 0.289 929 70118 −0.186 0.237 −0.004 0.944 1.043 0.042 / / 0.040 0.279 1025 70545 0.057 0.434 0.111 0.355 1.228 0.021 / / −0.060 0.418 1079 70686 −0.071 0.644 0.136 0.109 0.700 0.004 / / 0.014 0.571 1088 70803 0.173 0.197 −0.207 0.053 0.691 0.008 / / 0.067 0.094 1261 73438 0.397 0.057 −0.251 0.005 0.733 0.014 −0.056 0.542 −0.012 0.809 1077 73696 −0.384 0.425 −0.284 0.129 0.666 0.020 / / −0.097 0.154 1394 75705 0.570 0.049 0.019 0.797 0.477 0.165 0.213 0.337 −0.164 0.018 1210 76657 0.091 0.481 −0.370 0.031 0.744 0.019 −0.016 0.927 −0.038 0.395 1488 78386 0.092 0.010 −0.118 0.227 −0.578 0.034 / / 0.017 0.502 1475 78522 0.386 0.003 0.728 0.001 1.532 0.007 / / 0.170 0.038 If p<0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.

K. Limited Nitrogen Tolerance Screen

Under low nitrogen conditions, Arabidopsis seedlings become chlorotic and have less biomass. This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.

T2 seeds were plated on glufosinate selection plates containing 0.5× N-Free Hoagland's T 0.1 mM NH₄NO₃ T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (e.g., viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L. The leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system. A statistical logistic regression model was developed to predict an overall value based on five colors for each plant.

A list of recombinant DNA constructs that improve low nitrogen availability tolerance in plants illustrated in Table 13.

TABLE 13 Leaf color at day 21 Rosette weight NUC PEP Con- Risk at day 21 SEQ SEQ struct score P- Delta P- ID ID ID Orientation mean value mean value 188 991 10473 SENSE 4.078 0.017 −0.181 0.023 373 1176 11141 SENSE 4.800 0.027 −0.059 0.513 395 1198 11147 SENSE 3.499 0.012 −0.157 0.323 10 813 11860 ANTI-SENSE −3.108 0.157 0.345 0.017 781 1584 11933 ANTI-SENSE 0.412 0.024 0.004 0.902 661 1464 12123 ANTI-SENSE 4.867 0.025 0.036 0.750 8 811 12147 ANTI-SENSE 2.164 0.134 0.074 0.007 6 809 12217 SENSE 3.494 0.047 0.086 0.245 12 815 12230 SENSE 1.878 0.077 0.111 0.015 799 1602 12444 SENSE 0.144 0.926 0.014 0.010 21 824 12749 ANTI-SENSE 0.315 0.022 0.109 0.325 3 806 12816 SENSE −0.989 0.012 0.098 0.002 38 841 13038 ANTI-SENSE 2.207 0.450 0.074 0.040 39 842 13040 ANTI-SENSE 3.223 0.039 0.137 0.241 608 1411 13302 ANTI-SENSE 2.956 0.013 0.040 0.100 35 838 13828 ANTI-SENSE 3.733 0.002 −0.043 0.188 46 849 14340 ANTI-SENSE 3.417 0.023 −0.113 0.049 32 835 14405 SENSE 2.350 0.158 0.097 0.031 43 846 14415 SENSE 3.195 0.006 −0.131 0.066 85 888 14915 ANTI-SENSE 3.923 0.005 −0.081 0.079 78 881 15129 SENSE 3.751 0.002 0.096 0.164 104 907 15507 ANTI-SENSE 8.130 0.013 −0.086 0.312 106 909 15959 ANTI-SENSE 5.694 0.032 −0.165 0.121 98 901 16204 SENSE 7.476 0.013 −0.012 0.416 95 898 16309 SENSE 0.678 0.046 0.072 0.436 65 868 16323 SENSE 2.085 0.019 −0.008 0.779 16 819 17806 ANTI-SENSE 3.639 0.036 −0.087 0.208 184 987 18319 SENSE 1.043 0.023 −0.100 0.061 147 950 19154 SENSE −1.213 0.201 0.146 0.033 175 978 19240 SENSE 0.175 0.828 0.098 0.002 289 1092 71622 SENSE 0.222 0.357 0.082 0.003 287 1090 71637 SENSE 0.074 0.772 0.061 0.001 261 1064 71810 SENSE 2.561 0.010 −0.038 0.111 416 1219 74350 SENSE 8.315 0.006 0.020 0.504 500 1303 74573 SENSE 4.232 0.015 0.093 0.207 555 1358 74836 SENSE 1.278 0.002 −0.133 0.018 561 1364 74918 SENSE 5.122 0.022 0.414 0.346 27 830 75958 SENSE 1.827 0.046 −0.078 0.101 731 1534 76321 SENSE 5.099 0.004 −0.120 0.313 754 1557 76821 SENSE 4.293 0.011 −0.157 0.044 757 1560 76894 SENSE 3.806 0.048 0.123 0.102 513 1316 77041 SENSE 1.772 0.042 −0.186 0.098 786 1589 77250 SENSE 7.658 0.015 0.035 0.664 620 1423 77541 SENSE 1.896 0.045 −0.189 0.081 746 1549 77842 SENSE 4.863 0.048 −0.184 0.037 670 1473 77966 SENSE 1.716 0.120 0.218 0.022 719 1522 78191 SENSE 2.686 0.037 0.121 0.113 695 1498 78548 SENSE 1.766 0.191 0.116 0.027 226 1029 19775 SENSE 0.037 0.858 0.240 0.042 34 837 70721 ANTI-SENSE 1.858 0.012 0.052 0.047 280 1083 71696 SENSE −0.133 0.002 0.085 0.049

For rosette weight, if p<0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p<0.2. For root length, if p<0.05, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2, the transgenic plants showed a trend of trait enhancement as compared to the reference.

Transgenic plants comprising recombinant DNA expressing a protein as set forth in 807, 808, 817, 820, 829, 839, 847, 848, 850, 854, 858, 859, 866, 872, 875, 878, 889, 902, 908, 911, 922, 938, 944, 953, 963, 974, 980, 993, 1001, 1009, 1035, 1042, 1048, 1049, 1054, 1058, 1068, 1076, 1088, 1094, 1096, 1098, 1103, 1104, 1107, 1112, 1113, 1114, 1121, 1152, 1166, 1175, 1192, 1204, 1207, 1215, 1218, 1240, 1246, 1251, 1256, 1266, 1269, 1281, 1283, 1290, 1296, 1298, 1344, 1345, 1356, 1389, 1396, 1400, 1404, 1409, 1425, 1428, 1438, 1441, 1442, 1454, 1477, 1479, 1484, 1492, 1500, 1511, 1515, 1518, 1521, 1537, 1563, 1567, 1571, 1579, or 1603 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.

L. Statistic Analysis for Qualitative Responses

A list of responses that were analyzed as qualitative responses illustrated in Table 14.

TABLE 14 response Screen categories (success vs. failure) Wilting response Risk Soil drought tolerance screen non-wilted vs. wilted Score growth stage at day 14 heat stress tolerance screen 50% of plants reach stage 1.03 vs. not growth stage at day 14 salt stress tolerance screen 50% of plants reach stage 1.03 vs. not growth stage at day 14 PEG induced osmotic stress 50% of plants reach stage 1.03 vs. tolerance screen not growth stage at day 7 cold germination tolerance screen 50% of plants reach stage 0.5 vs. not number of rosette Shade tolerance screen 5 leaves appeared vs. not leaves at day 23 Flower bud formation at Shade tolerance screen flower buds appear vs. not day 23 leaf angle at day 23 Shade tolerance screen >60 degree vs. <60 degree number of green leaves limited nitrogen tolerance screen 6 or 7 leaves appeared vs. not at day 21 number of rosette limited nitrogen tolerance screen 6 or 7 leaves appeared vs. not leaves at day 21 Flower bud formation at limited nitrogen tolerance screen flower buds appear vs. not day 21

Plants were grouped into transgenic and reference groups and were scored as success or failure according to Table 14. First, the risk (R) was calculated, which is the proportion of plants that were scored as of failure plants within the group. Then the relative risk (RR) was calculated as the ratio of R (transgenic) to R (reference). Risk score (RS) was calculated as −log₂ ^(RR). Two criteria were used to determine a transgenic with enhanced trait(s). Transgenic plants comprising recombinant DNA disclosed herein showed trait enhancement according to either or both of the two criteria.

For the first criteria, the risk scores from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). RS with a value greater than 0 indicates that the transgenic plants perform better than the reference. RS with a value less than 0 indicates that the transgenic plants perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p<0.05 and risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.

For the second criteria, the RS from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). The RS with a value greater than 0 indicates that the transgenic plants from this event \ perform better than the reference. The RS with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference. If p<0.05 and risk score mean >0, the transgenic plants from this event showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed improvement in the same response, the transgene was deemed to show trait enhancement.

M. Statistic Analysis for Quantitative Responses

A list of responses that were analyzed as quantitative responses illustrated in Table 15.

TABLE 15 response screen seed yield Soil drought stress tolerance screen seedling weight at day 14 heat stress tolerance screen root length at day 14 heat stress tolerance screen seedling weight at day 14 salt stress tolerance screen root length at day 14 salt stress tolerance screen root length at day 11 salt stress tolerance screen seedling weight at day 14 PEG induced osmotic stress tolerance screen root length at day 11 PEG induced osmotic stress tolerance screen root length at day 14 PEG induced osmotic stress tolerance screen rosette area at day 8 cold shock tolerance screen rosette area at day 28 cold shock tolerance screen difference in rosette area from cold shock tolerance screen day 8 to day 28 root length at day 28 cold germination tolerance screen seedling weight at day 23 Shade tolerance screen petiole length at day 23 Shade tolerance screen root length at day 14 Early plant growth and development screen Seedling weight at day 14 Early plant growth and development screen Rosette dry weight at day 53 Late plant growth and development screen rosette radius at day 25 Late plant growth and development screen seed dry weight at day 58 Late plant growth and development screen silique dry weight at day 53 Late plant growth and development screen silique length at day 40 Late plant growth and development screen Seedling weight at day 21 Limited nitrogen tolerance screen Root length at day 21 Limited nitrogen tolerance screen

The measurements (M) of each plant were transformed by log₂ calculation. The Delta was calculated as log₂M(transgenic)−log₂M(reference). Two criteria were used to determine trait enhancement. A transgene of interest could show trait enhancement according to either or both of the two criteria. The measurements (M) of each plant were transformed by log₂ calculation. The Delta was calculated as log₂M(transgenic)−log₂M(reference). If the measured response was Petiole Length for the Low Light assay, Delta was subsequently multiplied by −1, to account for the fact that a shorter petiole length is considered an indication of trait enhancement.

For the first criteria, the Deltas from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference. Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p<0.05 and risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.

For the second criteria, the delta from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). The Delta with a value greater than 0 indicates that the transgenic plants from this event perform better than the reference. The Delta with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference. If p<0.05 and delta mean >0, the transgenic plants from this event showed statistically significant trait improvement as compared to the reference. If p<0.2 and delta mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed enhancement in the same response, the transgene was deemed to show trait improvement.

Example 2 Plant Expression Constructs

This example illustrates the construction of plasmids for transferring recombinant DNA into a plant cell nucleus that can be regenerated into transgenic plants.

Plant Expression Constructs for Corn Transformation

A base corn transformation vector pMON93039, as set forth in SEQ ID NO: 94614, illustrated in Table 16 and FIG. 1 , is made for use in preparing recombinant DNA for Agrobacterium-mediated transformation into corn tissue.

TABLE 16 Coordinates of SEQ ID NO: Function Name Annotation 94614 Agro- B-AGRtu.right Agro right border sequence, 11364-11720 bacterium border essential for transfer of T- T-DNA DNA. transfer Gene of E-Os.Act1 Upstream promoter region  19-775 interest of the rice actin 1 gene expression E- Duplicated35S A1-B3  788-1120 cassette CaMV.35S. domain without TATA box 2xA1-B3 P-Os.Act1 Promoter region of the rice 1125-1204 actin 1 gene L-Ta.Lhcb1 5′ untranslated leader of 1210-1270 wheat major chlorophyll a/b binding protein I-Os.Act1 First intron and flanking 1287-1766 UTR exon sequences from the rice actin 1 gene T-St.Pis4 3′ non-translated region of 1838-2780 the potato proteinase inhibitor II gene which functions to direct polyadenylation of the mRNA Plant P-Os.Act1 Promoter from the rice actin 2830-3670 selectable 1 gene marker L-Os.Act1 First exon of the rice actin 1 3671-3750 expression gene cassette I-Os.Act1 First intron and flanking 3751-4228 UTR exon sequences from the rice actin 1 gene TS-At.ShkG- Transit peptide region of 4238-4465 CTP2 Arabidopsis EPSPS CR-AGRtu. Coding region for bacterial 4466-5833 aroA-CP4.nat strain CP4 native aroA gene. T-AGRtu.nos A 3′ non-translated region of 5849-6101 the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Agro- B-AGRtu.left Agro left border sequence, 6168-6609 bacterium border essential for transfer of T- T-DNA DNA. transfer OR-Ec.oriV- The vegetative origin of 6696-7092 Maintenance RK2 replication from plasmid in E. coli RK2. CR-Ec.rop Coding region for repressor 8601-8792 of primer from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori- The minimal origin of 9220-9808 ColE1 replication from the E. coli plasmid ColE1. P-Ec.aadA- Promoter for Tn7 10339-10380 SPC/STR adenylyltransferase (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 10381-11169 SPC/STR adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA- 3′ UTR from the Tn7 11170-11227 SPC/STR adenylyltransferase (AAD(3″)) gene of E. coli.

Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of the base vector.

B. Plant Expression Constructs for Soy and Canola Transformation

Vectors for use in transformation of soybean and canola can also be prepared. Elements of an exemplary common expression vector pMON82053 (SEQ ID NO: 94615) are shown in Table 17 below and FIG. 2 .

TABLE 17 Coordinates of SEQ ID NO: Function Name Annotation 94615 Agrobacterium B-AGRtu.left Agro left border sequence, essential 6144-6585 T-DNA transfer border for transfer of T-DNA. Plant selectable P-At.Act7 Promoter from the Arabidopsis actin 6624-7861 marker 7 gene expression L-At.Act7 5′ UTR of Arabidopsis Act7 gene cassette I-At.Act7 Intron from the Arabidopsis actin7 gene TS-At.ShkG- Transit peptide region of 7864-8091 CTP2 Arabidopsis EPSPS CR-AGRtu.aroA- Synthetic CP4 coding region with 8092-9459 CP4.nno_At dicot preferred codon usage. T-AGRtu.nos A 3′ non-translated region of the 9466-9718 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Gene of interest P-CaMV.35S-enh Promoter for 35S RNA from CaMV  1-613 expression containing a duplication of the −90 to cassette −350 region. T-Gb.E6-3b 3′ untranslated region from the fiber 688-1002 protein E6 gene of sea-island cotton. Agrobacterium B-AGRtu.right Agro right border sequence, 1033-1389 T-DNA transfer border essential for transfer of T-DNA. Maintenance in OR-Ec.oriV-RK2 The vegetative origin of replication 5661-6057 E. coli from plasmid RK2. CR-Ec.rop Coding region for repressor of primer from the ColE1 plasmid. 3961-4152 Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of replication 2945-3533 from the E. coli plasmid ColE1. P-Ec.aadA- Promoter for Tn7 2373-2414 SPC/STR adenylyltransferase (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 SPC/STR adenylyltransferase (AAD(3″)) 1584-2372 conferring spectinomycin and streptomycin resistance. T-Ec.aadA- 3′ UTR from the Tn7 1526-1583 SPC/STR adenylyltransferase (AAD(3″)) gene of E. coli. Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of the base vector.

C. Cotton Transformation Vector

Plasmids for use in transformation of cotton tissue are prepared with elements of expression vector pMON99053 (SEQ ID NO: 94616) are shown in Table 18 below and FIG. 3 . Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression-cassette of the base vector.

TABLE 18 Coordinates of SEQ ID Function Name Annotation NO: 94616 Agrobacterium B-AGRtu.right Agro right border sequence,  1-357 T-DNA transfer border essential for transfer of T- DNA. Gene of interest Exp-CaMV. Enhanced version of the 35S  388-1091 cassette 35S-enh + RNA promoter from CaMV expression Ph.DnaK plus the petunia hsp70 5′ untranslated region T-Ps.RbcS2- The 3′ non-translated region 1165-1797 E9 of the pea RbcS2 gene which functions to direct polyadenylation of the mRNA. Plant selectable Exp- Promoter and 5′ untranslated 1828-2151 marker CaMV.35S region from the 35S RNA of expression CaMV cassette CR-Ec.nptII- Coding region for neomycin 2185-2979 Tn5 phosphotransferase gene from transposon Tn5 which confers resistance to neomycin and kanamycin. T-AGRtu.nos A 3′ non-translated region of 3011-3263 the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Agrobacterium B-AGRtu.left Agro left border sequence, 3309-3750 T-DNA transfer border essential for transfer of T- DNA. Maintenance in OR-Ec.oriV- The vegetative origin of 3837-4233 E. coli RK2 replication from plasmid RK2. CR-Ec.rop Coding region for repressor 5742-5933 of primer from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori- The minimal origin of 6363-6949 ColE1 replication from the E. coli plasmid ColE1. P-Ec.aadA- Promoter for Tn7 7480-7521 SPC/STR adenylyltransferase (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 7522-8310 SPC/STR adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA- 3′ UTR from the Tn7 8311-8368 SPC/STR adenylyltransferase (AAD(3″)) gene of E. coli.

Example 3 Corn Transformation

This example illustrates transformation methods in producing a transgenic nucleus in a corn plant cell and the plants, seeds and pollen produced from a transgenic cell with such a nucleus having an enhanced trait, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plasmid vectors are prepared by cloning DNA identified in Table 2 in the base vector for use in corn transformation of corn tissue.

For Agrobacterium-mediated transformation of corn embryo cells corn plants of a readily transformable line are grown in the greenhouse and ears are harvested when the embryos are 1.5 to 2.0 mm in length. Ears are surface sterilized by spraying or soaking the ears in 80% ethanol, followed by air drying. Immature embryos are isolated from individual kernels on surface sterilized ears. Prior to inoculation of maize cells, Agrobacterium cells are grown overnight at room temperature. Immature maize embryo cells are inoculated with Agrobacterium shortly after excision, and incubated at room temperature with Agrobacterium for 5-20 minutes. Immature embryo plant cells are then co-cultured with Agrobacterium for 1 to 3 days at 23° C. in the dark. Co-cultured embryos are transferred to selection media and cultured for approximately two weeks to allow embryogenic callus to develop. Embryogenic callus is transferred to culture medium containing 100 mg/L paromomycin and subcultured at about two week intervals. Transformed plant cells are recovered 6 to 8 weeks after initiation of selection.

For Agrobacterium-mediated transformation of maize callus immature embryos are cultured for approximately 8-21 days after excision to allow callus to develop. Callus is then incubated for about 30 minutes at room temperature with the Agrobacterium suspension, followed by removal of the liquid by aspiration. The callus and Agrobacterium are co-cultured without selection for 3-6 days followed by selection on paromomycin for approximately 6 weeks, with biweekly transfers to fresh media. Paromomycin resistant calli are identified about 6-8 weeks after initiation of selection.

For transformation by microprojectile bombardment maize immature embryos are isolated and cultured 3-4 days prior to bombardment. Prior to microprojectile bombardment, a suspension of gold particles is prepared onto which the desired recombinant DNA expression cassettes are precipitated. DNA is introduced into maize cells as described in U.S. Pat. Nos. 5,550,318 and 6,399,861 using the electric discharge particle acceleration gene delivery device. Following microprojectile bombardment, tissue is cultured in the dark at 27° C. Additional transformation methods and materials for making transgenic plants of this invention, for example, various media and recipient target cells, transformation of immature embryos and subsequence regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636, 6,232,526 and 7,151,204, which are incorporated herein by reference.

To regenerate transgenic corn plants a callus of transgenic plant cells resulting from transformation and selection is placed on media to initiate shoot development into plantlets which are transferred to potting soil for initial growth in a growth chamber at 26° C. followed by a mist bench before transplanting to 5 inch pots where plants are grown to maturity. The regenerated plants are self-fertilized and seed is harvested for use in one or more methods to select seeds, seedlings or progeny second generation transgenic plants (R2 plants) or hybrids, e.g. by selecting transgenic plants exhibiting an enhanced trait as compared to a control plant.

Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 7.

Example 4 Soybean Transformation

This example illustrates plant transformation in producing the transgenic soybean plants of this invention and the production and identification of transgenic seed for transgenic soybean having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

For Agrobacterium mediated transformation, soybean seeds are imbided overnight and the meristem explants excised. The explants are placed in a wounding vessel. Soybean explants and induced Agrobacterium cells from a strain containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette are mixed no later than 14 hours from the time of initiation of seed imbibition, and wounded using sonication. Following wounding, explants are placed in co-culture for 2-5 days at which point they are transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots. Resistant shoots are harvested approximately 6-8 weeks and placed into selective rooting media for 2-3 weeks. Shoots producing roots are transferred to the greenhouse and potted in soil. Shoots that remain healthy on selection, but do not produce roots are transferred to non-selective rooting media for an additional two weeks. Roots from any shoots that produce roots off selection are tested for expression of the plant selectable marker before they are transferred to the greenhouse and potted in soil. Additionally, a DNA construct can be transferred into the genome of a soybean cell by particle bombardment and the cell regenerated into a fertile soybean plant as described in U.S. Pat. No. 5,015,580, herein incorporated by reference.

Transgenic soybean plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 10.

Example 5 Cotton Transgenic Plants with Enhanced Agronomic Traits

Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797. Transgenic cotton plants containing each recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 803 are obtained by transforming with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants. Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, e.g. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g. irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of −14 to −18 bars, and growing a second set of transgenic and control plants under “dry” conditions, e.g. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.

The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.

Example 6 Canola Transformation

This example illustrates plant transformation in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

Tissues from in vitro grown canola seedlings are prepared and inoculated with overnight-grown Agrobacterium cells containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium, the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterization is performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants. Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant

Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 1. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 7.

Example 7 Identification of Homologs

This example illustrates the identification of homologs of proteins encoded by the DNA identified in Table 1 which is used to provide transgenic seed and plants having enhanced agronomic traits. From the sequence of the homologs, homologous DNA sequence can be identified for preparing additional transgenic seeds and plants of this invention with enhanced agronomic traits.

An “All Protein Database” is constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a polynucleotide sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; it is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.

The All Protein Database is queried using amino acid sequences provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606 using NCBI “blastp” program with E-value cutoff of 1e-8. Up to 1000 top hits are kept, and separated by organism names. For each organism other than that of the query sequence, a list is kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes of the polynucleotides provided herein, and is referred to as the Core List. Another list is kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.

The Organism Protein Database is queried using polypeptide sequences provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606 using NCBI “blastp” program with E-value cutoff of 1e⁻⁴. Up to 1000 top hits are kept. A BLAST searchable database is constructed based on these hits, and is referred to as “SubDB”. SubDB is queried with each sequence in the Hit List using NCBI “blastp” program with E-value cutoff of 1e⁻⁸. The hit with the best E-value is compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Likely orthologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 1607 to SEQ ID NO: 94613. These orthologs are reported in Tables 19 as homologs to the proteins cognate to genes used in trait-improving recombinant DNA

Example 8 Consensus Sequence Build

ClustalW program is selected for multiple sequence alignments of an amino acid sequence of SEQ ID NO: 804 and its homologs, through SEQ ID NO: 1606 and its homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. The consensus sequence of SEQ ID NO: 1325 and its 30 homologs were derived according to the procedure described above and is displayed in FIG. 4 .

Example 9 Pfam Module Annoation

This example illustrates the identification of domain and domain module by Pfam analysis.

The amino acid sequence of the expressed proteins that were shown to be associated with an enhanced trait were analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software. The Pfam domain modules and individual protein domain for the proteins of SEQ ID NO: 804 through 1606 are shown in Table 20 and Table 21 respectively. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 830 is characterized by two Pfam domains, e.g. “Lectin_legB” and “Pkinase”. See also the protein with amino acids of SEQ ID NO: 817 which is characterized by four copies of the Pfam domain “Arm”. In Table 21 “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 22.

TABLE 20 PEP Seq ID No. Construct ID Pfam module Position 804 CGPG10.pep p450  31-495 805 CGPG1008.pep Tryp_alpha_amyl 23-95 806 CGPG1023.pep Na_Ca_ex::Na_Ca_ex 104-255::299-432 807 CGPG1038.pep DUF1475  1-256 812 CGPG1113.pep DUF1350  49-370 814 CGPG1163.pep DSPc  49-182 817 CGPG1205.pep Arm::Arm::Arm::Arm 94-134::135- 175::176-216::258- 298 818 CGPG1207.pep NifU_N  26-105 820 CGPG1223.pep ATP_bind_1  7-250 821 CGPG1250.pep DUF822  12-160 824 CGPG1319.pep DUF599  10-233 826 CGPG1329.pep Cullin  29-631 827 CGPG133.pep Cyclin_N::Cyclin_C 168-293::295-422 828 CGPG1332.pep Cullin  12-646 829 CGPG1343.pep LRR_1 389-412 830 CGPG1348.pep Lectin_legB::Pkinase 27-248::334-604 831 CGPG1349.pep B_lectin::S_locus_glycop::PAN_1::Pkinase 65-171::180- 312::327-404::484- 731 832 CGPG1373.pep Pkinase  12-291 833 CGPG1377.pep Pkinase  4-258 834 CGPG1412.pep TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_ 45-221::243- C 376::431-578 835 CGPG1421.pep Biotin_lipoyl::E3_binding::2-oxoacid_dh 76-149::180- 218::249-480 836 CGPG1426.pep Aminotran_1_2  48-432 837 CGPG1433.pep Pyr_redox_2::Pyr_redox_dim 45-359::388-497 838 CGPG1453.pep malic::Malic_M 171-360::362-615 839 CGPG1454.pep Ribul_P_3_epim  7-207 840 CGPG1463.pep Alpha-amylase::Alpha-amyl_C2 26-361::362-422 841 CGPG1464.pep Glycolytic  11-358 842 CGPG1471.pep IF4E  1-198 843 CGPG1481.pep Pkinase  4-260 844 CGPG1499.pep PPDK_N::PEP-utilizers::PEP-utilizers_C 85-445::496- 586::598-955 845 CGPG150.pep p450  30-507 846 CGPG1536.pep CRAL_TRIO_N::CRAL_TRIO 73-142::159-345 847 CGPG1539.pep UPF0139  8-107 848 CGPG155.pep GlutR_N::Shikimate_DH::GlutR_dimer 100-251::255- 407::420-526 849 CGPG1583.pep PLAC8  88-187 850 CGPG1588.pep PLAC8  75-214 851 CGPG16.pep MIP  14-235 852 CGPG1609.pep. MMR_HSR1::DUF933 54-190::337-420 853 CGPG1629.pep WD40::WD40::WD40 262-301::307- 346::356-395 854 CGPG1637.pep DUF220 163-262 855 CGPG1653.pep TBC 200-415 856 CGPG1658.pep Nodulin-like  14-260 857 CGPG1663.pep BT1  30-441 858 CGPG1682.pep OPT  62-685 859 CGPG1701.pep Glyco_transf_8  76-299 861 CGPG1724.pep Per1  63-334 862 CGPG1726.pep DUF607 111-291 863 CGPG1736.pep Usp  1-148 864 CGPG1741.pep mTERF 279-627 865 CGPG1783.pep PB1  42-132 866 CGPG1790.pep PB1  59-153 868 CGPG1845.pep TFIID-18 kDa  29-119 869 CGPG1855.pep CAF1  3-227 870 CGPG1870.pep Pkinase 406-572 871 CGPG1879.pep Pkinase::NAF 21-277::303-364 872 CGPG1886.pep Pkinase  26-325 873 CGPG1903.pep F-box 320-367 874 CGPG1905.pep F-box::Kelch_2::Kelch_2 4-51::104- 150::255-306 875 CGPG1914.pep F-box::Kelch_1::Kelch_1 42-89::170- 215::217-266 876 CGPG193.pep WD40::WD40::WD40::WD40 167-205::268- 307::318-355::363- 401 877 CGPG1939.pep F-box::WD40::WD40::WD40 66-113::152- 190::247-283::325- 364 878 CGPG1949.pep YDG_SRA::Pre-SET::SET 360-519-543- 639-641-771 879 CGPG1959.pep PHD::SET 34-82::208-344 880 CGPG197.pep p450  40-481 882 CGPG1981.pep MT-A70 476-636 883 CGPG1999.pep Nfu_N::NifU 78-193::221-291 884 CGPG2.pep p450  71-531 885 CGPG2006.pep RCC1::RCC1::RCC1::RCC1 32-82-138- 187::190-239::294- 343 886 CGPG2010.pep Aminotran_5  74-448 887 CGPG2011.pep X8 128-209 888 CGPG2014.pep Pkinase::NAF 28-282::341-398 889 CGPG2023.pep Zip  48-352 890 CGPG2026.pep Pkinase  38-324 892 CGPG2064.pep Cenp-O 123-201 894 CGPG2077.pep NAC::UBA 88-147::195-232 895 CGPG2095.pep AARP2CN::DUF663 228-309::483-780 896 CGPG2105.pep Pkinase::Pkinase_C 102-404::422-471 897 CGPG2108.pep Response_reg::CCT 64-180::442-484 898 CGPG2111.pep polyprenyl_synt  74-324 899 CGPG2124.pep UIM::efhand 139-156::220-248 900 CGPG2125.pep Glutaredoxin  44-110 903 CGPG2134.pep ATP-synt_G  8-122 904 CGPG2139.pep DUF1517  94-391 905 CGPG2140.pep PhzC-PhzF  6-282 907 CGPG2163.pep Cupin_1::Cupin_1 5-157::190-339 908 CGPG2165.pep ClpS  76-152 910 CGPG2218.pep Spc97_Spc98  67-555 912 CGPG2225.pep EMP24_GP25L  52-116 913 CGPG2229.pep Subtilisin_N::PA 30-106::362-461 915 CGPG2254.pep Ribosomal_L7Ae  20-114 916 CGPG2268.pep CBS  66-188 917 CGPG227.pep p450  37-494 918 CGPG2312.pep UPF0061  75-571 919 CGPG2315.pep SIP1 286-514 920 CGPG2316.pep PTPA  98-396 922 CGPG235.pep p450  74-510 923 CGPG2358.pep Branch  54-278 925 CGPG2361.pep Metallophos  9-231 926 CGPG2365.pep Epimerase  3-211 927 CGPG2372.pep Pribosyltran  29-169 928 CGPG2374.pep Aminotran_5  8-370 929 CGPG2377.pep DAO  69-466 930 CGPG2387.pep H_PPase  1-239 931 CGPG2389.pep Carb_anhydrase  52-275 932 CGPG2395.pep AA_permease  89-526 934 CGPG2409.pep DUF862  17-154 935 CGPG2410.pep GST_N::GST_C 5-79::101-204 937 CGPG2416.pep Hin1  97-235 938 CGPG2441.pep Sina  5-205 939 CGPG2450.pep Epimerase 114-371 940 CGPG2451.pep RALF  57-129 941 CGPG2492.pep Pribosyltran  80-216 942 CGPG2495.pep ADH_N::ADH_zinc_N 25-134::165-307 943 CGPG2506.pep PfkB  5-289 944 CGPG2515.pep TIM  5-244 945 CGPG2531.pep AhpC-TSA  5-138 946 CGPG2581.pep SelR  12-133 947 CGPG2584.pep zf-Tim10_DDP 22-86 948 CGPG2592.pep TFIID_30 kDa 30-80 949 CGPG2612.pep RRM_1::RRM1::RRM_1 65-132::150- 225::275-343 950 CGPG2660.pep B3::B3 17-115::211-301 951 CGPG2663.pep NTF2::RRM_1 15-131::295-365 952 CGPG2679.pep ACBP::Ank::Ank 104-190::265- 297::298-330 953 CGPG2696.pep zf-C3HC4 177-218 954 CGPG2772.pep Mov34  6-136 955 CGPG2773.pep Asp 161-498 956 CGPG281.pep TLC  91-574 957 CGPG2846.pep Aldo_ket_red  49-365 958 CGPG2852.pep Glyoxalase  9-132 960 CGPG2870.pep zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf- 111-137::159- CCCH 185::205-231::347- 373::393-419 961 CGPG2877.pep LAG1  96-307 962 CGPG289.pep Cellulose_synt 243-1060 963 CGPG2924.pep zf-C3HC4 138-179 964 CGPG2947.pep Acetyltransf_1::Bromodomain 265-343::460-548 965 CGPG2963.pep C1_2::C1_3::C1_3::C1_2::C1_3::C1_3::C1_2 81-108::136- 164::194-223::305- 335::391-420::494- 522::552-581 966 CGPG2987.pep SRF-TF Nov-66 968 CGPG3045.pep Pkinase_Tyr  82-356 969 CGPG3046.pep AAA 121-305 970 CGPG3060.pep p450  67-528 971 CGPG3075.pep Auxin_inducible  7-106 972 CGPG310.pep Cyclin_N  18-143 973 CGPG3103.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR:: 14-48::49-83::84- PPR::PPR::PPR 118::119-153::155- 188::189-223::224- 258::259-293::295- 329::330-364::365- 398 974 CGPG315.pep p450  29-491 976 CGPG3189.pep RRM_1::RRM_1 115-186::209-280 977 CGPG3204.pep KH_1::KH_1::KH_1::KH_1::KH_1 45-104::151- 221::318-381::400- 467::575-637 978 CGPG3208.pep MATH::MATH 26-153::180-302 979 CGPG3219.pep 2OG-FeII_Oxy 220-320 980 CGPG3233.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR 160-194::195- 229::231-265::266- 300::301-335::336- 370::371-405::406- 440 981 CGPG3263.pep Tryp_alpha_amyl  28-104 982 CGPG3276.pep ECH  11-186 984 CGPG3282.pep Steroid_dh 117-268 985 CGPG3300.pep zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf- 55-72::74-91::93- CCHC::zf-CCHC::zf-CCHC 110::112-129::138- 155::157-174::229- 246 986 CGPG3318.pep Peptidase_C14  3-416 987 CGPG3319.pep AP2 28-79 988 CGPG3326.pep zf-C3HC4 259-299 989 CGPG333.pep PTS_2-RNA  48-239 990 CGPG3338.pep Alba 17-87 991 CGPG334.pep Mov34  20-128 992 CGPG3374.pep peroxidase  42-286 993 CGPG3402.pep Dimerisation::Methyltransf_2 30-89::99-342 995 CGPG3413.pep WD40::U3_snoRNA_C 168-207::377-523 996 CGPG3422.pep WD40::WD40::WD40 241-279::387- 425::519-559 997 CGPG3436.pep DUF6::DUF6 17-144::198-327 998 CGPG3539.pep Mito_carr::Mito_carr::Mito_carr 11-105::113- 209::214-303 999 CGPG3550.pep FAE1_CUT1_RppA::ACP_syn_III_C 81-370::384-468 1000 CGPG3551.pep Pkinase  9-273 1001 CGPG3552.pep Aldedh  23-441 1002 CGPG3572.pep FA_hydroxylase 112-225 1004 CGPG3599.pep DUF579  51-289 1008 CGPG364.pep zf-C3HC4  97-137 1010 CGPG3679.pep malic::Malic_M::PTA_PTB 36-179::181- 418::446-768 1011 CGPG3686.pep Gp_dh_N::Gp_dh_C 2-150::155-312 1012 CGPG3694.pep LRRNT_2:LRR_1::LRR_1:LRR_1:LRR_1:: 38-78::106- Pkinase_Tyr 128::130-152::154- 176::178-201::312- 583 1013 CGPG3696.pep MMR_HSR1 136-257 1014 CGPG3698.pep WD40::WD40 104-142::234-272 1015 CGPG3699.pep adh_short  19-187 1016 CGPG3702.pep SAM_1 228-291 1017 CGPG3703.pep ENOD93  25-103 1018 CGPG3707.pep Pkinase  42-333 1019 CGPG3710.pep VQ 118-148 1020 CGPG3730.pep DUF167 140-216 1021 CGPG3731.pep DUF616 194-508 1022 CGPG3734.pep PRK::Pribosyltran 46-233::280-425 1023 CGPG3745.pep RRM_1::RRM_1 386-455::481-553 1024 CGPG3764.pep Response_reg  20-145 1026 CGPG3851.pep SH3_1 284-338 1027 CGPG3911.pep Aldedh 104-587 1028 CGPG3948.pep NAP  50-295 1031 CGPG3996.pep Inositol_P  6-267 1032 CGPG4006.pep ENT  1-74 1033 CGPG4025.pep SQS_PSY  44-331 1034 CGPG4028.pep Transket_pyr::Transketolase_C 398-565::579-702 1035 CGPG403.pep Pkinase  78-336 1036 CGPG4041.pep DEAD::HelicasC 141-315::386-462 1037 CGPG4078.pep GST_C 180-283 1038 CGPG4079.pep RRS1  1-178 1041 CGPG4104.pep LRRNT_2:LRR_1::LRR_1::LRR_1:LRR_1:: 30-67::95- Pkinase 117::119-141::143- 165::167-188::367- 633 1042 CGPG4127.pep Hydrolase  43-239 1043 CGPG4135.pep Pkinase::efhand::efhand::efhand::efhand 118-376::423- 451::459-487::495- 523::529-557 1044 CGPG4161.pep Methyltransf_11  56-159 1045 CGPG4180.pep GHMP_kinases_N::GHMP_kinases_C 152-219::382-466 1046 CGPG4191.pep Bombesin 163-176 1047 CGPG4199.pep Copine::zf-C3HC4 117-265::385-417 1048 CGPG4241.pep GASA  3-99 1049 CGPG427.pep Pkinase_Tyr  8-262 1050 CGPG4273.pep dsrm::dsrm 2-68::88-153 1051 CGPG4301.pep 2OG-FeII_Oxy 151-253 1052 CGPG4303.pep Rhodanese  13-114 1053 CGPG4313.pep G6PD_N::G6PD_C 94-273::276-573 1054 CGPG4314.pep AWPM-19  15-156 1055 CGPG4329.pep AA_kinase  86-324 1056 CGPG4330.pep PALP  53-341 1057 CGPG4338.pep Proteasome  21-217 1058 CGPG4341.pep Mito_carr::Mito_carr::Mito_carr 51-134::158- 246::252-343 1061 CGPG4386.pep GHMP_kinases_N::GHMP_kinases_C 113-171::245-338 1062 CGPG4394.pep p450  39-503 1063 CGPG4396.pep p450  39-504 1064 CGPG4400.pep p450  32-474 1065 CGPG4401.pep p450  47-511 1066 CGPG441.pep Chalcone  14-225 1067 CGPG4413.pep p450  32-547 1068 CGPG4427.pep p450  57-530 1069 CGPG4446.pep p450  43-504 1070 CGPG4448.pep p450  32-486 1071 CGPG4474.pep Band_7  33-212 1072 CGPG4482.pep peroxidase  47-291 1073 CGPG4511.pep VHS::GAT 36-166::227-315 1074 CGPG4517.pep Aldo_ket_red  5-292 1075 CGPG4551.pep XS::XH 30-148::418-557 1077 CGPG4567.pep SRF-TF  3-53 1078 CGPG4586.pep RRM_1  8-73 1079 CGPG4600.pep zf-CCCH::zf-CCCH 13-39::149-174 1080 CGPG4631.pep C1_2::C1_2::C1_3::C1_2::C1_3::C1_2 88-115::209- 237::264-292::319- 349::404-433::566- 595 1081 CGPG4642.pep Pyridoxal_deC  63-412 1082 CGPG4645.pep Cu-oxidase_3::Cu-oxidase::Cu-oxidase_2 31-148::157- 325::414-551 1083 CGPG4646.pep efhand_like::PI-PLC-X::PI-PLC-Y::C2 27-105::108- 251::332-450::471- 563 1084 CGPG4649.pep SMP::SMP::SMP 14-72::130- 191::195-256 1085 CGPG4653.pep DUF1637  47-280 1087 CGPG4668.pep SYF2 140-306 1088 CGPG469.pep tRNA-synt_1c::tRNA-synt_1c_C 213-518::520-697 1089 CGPG4708.pep Sulfate_transp::STAS 172-482::505-623 1090 CGPG4712.pep Mem_trans  9-565 1091 CGPG4714.pep DUF231 248-423 1092 CGPG4719.pep Response_reg::CCT 37-153::417-461 1093 CGPG473.pep Peptidase_M16::Peptidase_M16_C 88-234::239-423 1094 CGPG4734.pep Auxin_inducible  19-119 1095 CGPG4736.pep Pribosyltran 225-358 1096 CGPG474.pep Pro_isomerase  6-172 1102 CGPG4850.pep PMEI  25-174 1103 CGPG4868.pep PsbW  1-133 1104 CGPG4871.pep Tryp_alpha_amyl  52-133 1105 CGPG488.pep Histone 19-92 1106 CGPG4908.pep WD40::WD40 16-54::63-101 1108 CGPG4921.pep WD40::WD40::WD40::WD40::WD40 202-241::253- 291::295-333::337- 375::472-510 1109 CGPG4954.pep LRRNT_2::LRR_1::LRR_1::LRR_1 33-72::76-98::100- 122::124-145 1110 CGPG4956.pep Asp 141-482 1111 CGPG4959.pep adh_short  15-183 1112 CGPG4965.pep zf-A20::zf-AN1 15-39::114-154 1113 CGPG4970.pep GASA  1-108 1114 CGPG4980.pep U-box::Arm::Arm 73-147::246- 287::288-328 1115 CGPG4982.pep F-box::FBA_1 2-49::209-387 1116 CGPG4985.pep CPSase_sm_chain::GATase 56-203::245-422 1117 CGPG4990.pep LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1:: 73-112::139- LRR_1 161::163-183::187- 206::210-232::306- 328 1118 CGPG4991.pep PALP 164-473 1119 CGPG5007.pep adh_short  21-192 1120 CGPG5015.pep adh_short  13-126 1121 CGPG5026.pep adh_short  46-221 1122 CGPG5029.pep adh_short  80-252 1123 CGPG5046.pep LRRNT_2::LRR_1::LRR_1::LRR_1::Pkinase 30-70::99- 121::123-145::147- 169::306-573 1124 CGPG508.pep Na_sulph_symp  93-563 1125 CGPG5103.pep C2  9-95 1126 CGPG511.pep Rho_GDI  22-222 1127 CGPG5121.pep efhand_like::PI-PLC-X::PI-PLC-Y::C2 30-113::116- 258::331-449::470- 562 1128 CGPG5126.pep peroxidase  54-303 1129 CGPG5136.pep p450  35-500 1130 CGPG5146.pep p450  45-501 1131 CGPG5149.pep p450  31-478 1132 CGPG5181.pep Pkinase 278-540 1133 CGPG52.pep Sugar_tr  32-472 1134 CGPG5206.pep UDPG_MGDP_dh_N::UDPG_MGDP_dh:: 2-200::209- UDPG_MGDP_dh_C 306::328-452 1136 CGPG5232.pep Pkinase  71-328 1137 CGPG5239.pep Copine 136-284 1138 CGPG5246.pep ABC_tran::ABC_tran 94-285::406-571 1139 CGPG525.pep CDP-OH_P_transf 138-277 1140 CGPG5268.pep CDC50  65-368 1141 CGPG5272.pep AA_permease 153-621 1142 CGPG5333.pep MFS_1  55-468 1143 CGPG5338.pep RRM_1::RRM_1 8-77::108-178 1144 CGPG5341.pep F-box 33-79 1145 CGPG5369.pep AA_kinase::ACT::ACT 83-366::400- 469::477-539 1146 CGPG5372.pep SBF 142-322 1147 CGPG5380.pep Tyr-DNA_phospho 137-581 1148 CGPG5386.pep MOSC_N::MOSC 4-132::138-296 1149 CGPG5396.pep PALP_V  9-297 1150 CGPG5397.pep PDT 128-307 1151 CGPG5421.pep Pre-SET::SET 119-267::269-414 1152 CGPG5433.pep MtN3_slv::MtN3_slv 10-98::132-218 1153 CGPG5439.pep LANC_like  69-410 1154 CGPG5453.pep Mito_carr::Mito_carr::Mito_carr 14-116::125- 215::233-334 1155 CGPG5456.pep Mito_carr::Mito_carr::Mito_carr 78-175::183- 279::283-373 1156 CGPG5483.pep PP2C  66-369 1157 CGPG5492.pep FAE1_CUT1_RppA::ACP_syn_III_C 61-358::372-456 1158 CGPG5508.pep RCC1::RCC1::RCC1::RCC1::FYVE::DZC 310-359::413- 462::478-526::582- 630::633-701::  967-1002 1159 CGPG5520.pep TFIID-31 kDa  19-152 1160 CGPG5525.pep PRMT5 187-679 1161 CGPG5526.pep Pkinase  8-295 1162 CGPG5530.pep Response_reg 504-644 1163 CGPG5534.pep Y_phosphatase2  3-169 1164 CGPG5537.pep TBP::TBP 62-147::152-238 1165 CGPG5545.pep CBS::CBS 35-175::193-318 1166 CGPG555.pep PALP::Thr_dehydrat_C::Thr_dehydrat_C 104-396::409- 498::504-591 1167 CGPG5558.pep Cyclin_N::Cyclin_C 212-337::339-458 1168 CGPG5559.pep Sue_Fer-like  69-311 1169 CGPG5562.pep Sue_Fer-like  59-308 1170 CGPG5592.pep Rho_GDI  35-239 1171 CGPG5625.pep LRR_1::LRR_1::Pkinase 433-455::457- 476::586-854 1172 CGPG5631.pep WAK::Pkinase 171-270::390-658 1173 CGPG5632.pep Aldedh  29-491 1174 CGPG5636.pep Aldedh  15-476 1175 CGPG5637.pep Aldedh  32-493 1176 CGPG564.pep Aminotran_3  80-413 1177 CGPG5641.pep Aldedh  14-472 1178 CGPG5650.pep Aminotran_3  32-374 1179 CGPG5653.pep Aminotran_1_2  32-383 1180 CGPG5657.pep Aldedh  15-474 1181 CGPG5671.pep Gp_dh_N::Gp_dh_C 3-151::156-313 1182 CGPG5672.pep Glutaminase  24-309 1183 CGPG5677.pep PGAM  4-165 1184 CGPG5678.pep Aminotran_1_2  35-385 1185 CGPG5679.pep TIM  7-248 1186 CGPG5682.pep Aminotran_3  31-384 1187 CGPG5691.pep PK::PK_C 5-350::362-478 1188 CGPG5699.pep Gp_dh_N::Gp_dh_C 3-155::160-316 1189 CGPG5705.pep NDK  3-137 1190 CGPG5722.pep Pyrophosphatase  17-175 1191 CGPG5734.pep Cyclin_N::Cyclin_C 232-357::359-478 1192 CGPG5736.pep PP2C  22-280 1193 CGPG5744.pep CDC50  63-365 1194 CGPG5747.pep Pkinase  23-318 1195 CGPG5748.pep NAD_Gly3P_dh_N::NAD_Gly3P_dh_C 84-259::282-432 1198 CGPG577.pep Thioredoxin  7-111 1199 CGPG5780.pep AA_permease  68-517 1200 CGPG5793.pep AA_permease 285-815 1201 CGPG5795.pep Sugar_tr 123-565 1202 CGPG5796.pep Sugar_tr  43-466 1203 CGPG5800.pep AA_permease  86-546 1204 CGPG5812.pep Pkinase  22-273 1205 CGPG5815.pep Pkinase  9-272 1206 CGPG5838.pep Pkinase  1-264 1207 CGPG5844.pep Pkinase  78-351 1208 CGPG5846.pep Pkinase  99-376 1209 CGPG5851.pep Pkinase 121-401 1210 CGPG5857.pep Pkinase  19-273 1211 CGPG5862.pep Pkinase 181-447 1212 CGPG5863.pep Pkinase  52-330 1213 CGPG5867.pep Pkinase 142-423 1214 CGPG5872.pep Pkinase  18-288 1215 CGPG5913.pep ADH_N::ADH_zinc_N 28-109::140-284 1217 CGPG5961.pep Biotin_lipoyl::2-oxoacid_dh 94-167::232-462 1219 CGPG5968.pep Pribosyltran  36-172 1220 CGPG5984.pep Pkinase 115-443 1221 CGPG5991.pep LRR_1 266-293 1222 CGPG6006.pep RRM_1 19-89 1223 CGPG6015.pep La::RRM_1:RRM_3 14-85::118- 188::302-404 1224 CGPG603.pep G6PD_N::G6PD_C 35-222::224-508 1225 CGPG6046.pep Str_synth 179-266 1226 CGPG6063.pep Nramp  88-451 1228 CGPG6092.pep SRPRB  53-235 1229 CGPG6104.pep Steroid_dh 111-262 1230 CGPG6106.pep LEA_5  1-92 1231 CGPG6111.pep PP-binding  48-115 1232 CGPG6113.pep UQ_con  7-143 1234 CGPG6132.pep SMP::SMP::SMP 13-71::135- 196::200-262 1236 CGPG6147.pep Redoxin  74-234 1237 CGPG6152.pep Arf  5-177 1238 CGPG6154.pep Ion_trans_2::Ion_trans_2 122-204::253-328 1239 CGPG6170.pep UQ_con  19-158 1240 CGPG6171.pep Thioredoxin 120-227 1241 CGPG6177.pep AIG1  39-236 1242 CGPG6181.pep Peptidase_C12  2-214 1243 CGPG6188.pep Di19  10-217 1244 CGPG6202.pep TB2_DP1_HVA22  9-106 1245 CGPG6217.pep MFS_1::Sugar_tr 40-460::90-507 1246 CGPG623.pep SATase_N::Hexapep::Hexapep::Hexapep 45-149::203- 220::229-246::247- 264 1247 CGPG6239.pep Sugar_tr  27-458 1248 CGPG6244.pep Pkinase  39-303 1249 CGPG6254.pep Pkinase::NAF 12-264::292-352 1251 CGPG627.pep His_biosynth  48-289 1252 CGPG6271.pep Pkinase 191-527 1253 CGPG6278.pep Pkinase  86-368 1254 CGPG6288.pep Pkinase_Tyr 207-463 1255 CGPG6309.pep PRA1  29-181 1256 CGPG633.pep DCP1  12-134 1257 CGPG635.pep Epimerase  9-273 1258 CGPG6350.pep LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1 32-78::105- 127::129-151::153- 175::177-196 1260 CGPG6365.pep Aminotran_1_2  32-384 1261 CGPG6374.pep Gln-synt_C 120-380 1262 CGPG6377.pep PGK  2-383 1263 CGPG638.pep PA  51-163 1264 CGPG6397.pep F420_oxidored  3-246 1265 CGPG6398.pep Enolase_N::Enolase_C 5-135::140-430 1266 CGPG6408.pep ADH_N::ADH_zinc_N 25-155::185-350 1267 CGPG6415.pep NTP_transferase  4-271 1268 CGPG6421.pep ADH_N::ADH_zinc_N 25-148::179-318 1269 CGPG6442.pep iPGM_N::Metalloenzyme 2-363::373-488 1270 CGPG6443.pep PGK  1-391 1271 CGPG6446.pep PK::PK_C 106-453::467-587 1272 CGPG6453.pep Aminotran_1_2  41-402 1273 CGPG6466.pep ADH_N::ADH_zinc_N 27-153::184-322 1274 CGPG6467.pep Aminotran_3  19-366 1275 CGPG6470.pep PfkB  1-302 1276 CGPG6475.pep NTP_transferase  10-282 1277 CGPG6477.pep NDK  4-138 1278 CGPG6478.pep PfkB  1-308 1279 CGPG6493.pep AA_permease  94-561 1280 CGPG6506.pep Asparaginase 140-457 1281 CGPG6518.pep NAD_binding_2::6PGD 2-173::177-467 1282 CGPG6546.pep PK::PK_C 3-348::360-477 1283 CGPG6556.pep Aminotran_1_2 124-475 1284 CGPG6562.pep Aminotran_3 116-451 1285 CGPG6566.pep NTP_transferase::Hexapep::Hexapep::Hexapep 95-350::398- 415::432-449::460- 477 1286 CGPG6571.pep Aldedh 102-560 1287 CGPG6576.pep Aldedh  99-565 1288 CGPG659.pep G_glu_transpept  48-567 1289 CGPG6594.pep Pyr_redox_2::Pyr_redox_dim 94-419::450-559 1290 CGPG6603.pep Pyr_redox_2::Pyr_redox_dim 94-397::427-538 1291 CGPG6608.pep Pyr_redox_2::Pyr_redox_dim 93-394::423-532 1292 CGPG6634.pep DUF177 100-252 1294 CGPG6667.pep Invertase_neut  89-577 1295 CGPG6678.pep Biotin_lipoyl::E3_binding::2-oxoacid_dh 92-165::225- 263::281-512 1296 CGPG6695.pep Pyr_redox_2::Pyr_redox_dim 97-408::436-545 1297 CGPG6699.pep Ribul_P_3_epim  94-295 1298 CGPG670.pep Fer2  60-135 1299 CGPG6705.pep PK::PK_C::PEP-utilizers 89-433::445- 559::584-663 1300 CGPG6735.pep FBPase  93-413 1301 CGPG6744.pep Glycolytic  92-429 1302 CGPG6753.pep Pyr_redox_2 236-538 1303 CGPG6757.pep Aminotran_1_2 127-473 1305 CGPG6806.pep mTERF 110-457 1306 CGPG6811.pep GH3  10-567 1308 CGPG6815.pep V-ATPase_G  5-109 1310 CGPG6830.pep Tbf5 13-76 1313 CGPG6864.pep DUF620 190-438 1314 CGPG6877.pep Hep_59 101-194 1315 CGPG6878.pep Peptidase_M24 107-343 1316 CGPG6880.pep PAP_fibrillin  72-232 1318 CGPG6887.pep AIG2  12-111 1319 CGPG6895.pep zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC 166-183::208- 225::325-342::356- 373 1322 CGPG6912.pep zf-DHHC 149-213 1324 CGPG6942.pep RNA_pol_Rpb5_N::RNA_pol_Rpb5_C 18-108::149-222 1327 CGPG6969.pep 2OG-FeII_Oxy 223-323 1329 CGPG6991.pep Glyco_tran_28_C  11-170 1332 CGPG7037.pep Sad1_UNC 313-416 1333 CGPG7051.pep PAP_fibrillin  84-236 1336 CGPG7086.pep SFT2  44-163 1339 CGPG7136.pep NOI  1-72 1340 CGPG7147.pep RAMP4  1-64 1343 CGPG7222.pep Branch  49-274 1345 CGPG7233.pep eIF2A 214-407 1346 CGPG7238.pep UPF0185  5-80 1347 CGPG7253.pep ArfGap  15-117 1348 CGPG7255.pep Arf  5-177 1349 CGPG7286.pep ORC2  20-345 1350 CGPG7292.pep Methyltransf_11  38-135 1351 CGPG7301.pep ELFV_dehydrog_N::ELFV_dehydrog 57-187::202-445 1352 CGPG7305.pep Pyr_redox_2 126-386 1353 CGPG7307.pep Gp_dh_N::Gp_dh_C 11-163::168-324 1354 CGPG7318.pep MIP  1-142 1355 CGPG7319.pep SNF5 172-400 1356 CGPG7345.pep Lipase_3  97-237 1357 CGPG7368.pep MT-A70 516-676 1358 CGPG7385.pep FHA  32-107 1359 CGPG7391.pep G-patch  6-50 1360 CGPG7405.pep TATA_RF  1-216 1361 CGPG7415.pep IU_nuc_hydro  1-312 1362 CGPG7416.pep GLTP  52-233 1363 CGPG7420.pep PRK  95-302 1366 CGPG7445.pep PRC::PRC 92-169::171-252 1367 CGPG7465.pep Aldedh 103-567 1368 CGPG7473.pep F-box::WD40::WD40::WD40::WD40 273-320::412- 449::453-493::520- 556::560-598 1369 CGPG7489.pep UBX 295-376 1370 CGPG7492.pep Pescadillo_N::BRCT 8-291::337-414 1371 CGPG7499.pep G-alpha 423-839 1374 CGPG7508.pep Smg4_UPF3  1-170 1375 CGPG7509.pep SSB  76-187 1376 CGPG7511.pep GFA  31-125 4377 CGPG7515.pep Brix  45-297 1378 CGPG7521.pep G-alpha  23-386 1380 CGPG7547.pep PAD_porph  14-368 1381 CGPG7561.pep Snf7  17-187 1382 CGPG7562.pep Sybindin  6-136 1383 CGPG7563.pep DUF887  40-279 1384 CGPG7567.pep Peptidase_M18  14-461 1389 CGPG7597.pep zf-AN1  76-116 1390 CGPG7606.pep Pentapeptide::Pentapeptide 127-166::172-211 1392 CGPG7637.pep DAD  2-112 1393 CGPG7649.pep YgbB  71-227 1394 CGPG7658.pep Cyclase  56-256 1395 CGPG7664.pep Aldedh  9-463 1396 CGPG7666.pep Aminotran_1_2  26-392 1397 CGPG7668.pep DUF594 660-719 1399 CGPG7746.pep UPF0153  49-139 1400 CGPG7747.pep Copine 113-261 1401 CGPG7752.pep zf-MYND::PDCD2_C 176-214::241-403 1403 CGPG7770.pep YTH 263-353 1406 CGPG7778.pep Ubie_methyltran  51-304 1407 CGPG7786.pep KH_1 141-193 1408 CGPG7788.pep YIF1  34-263 1410 CGPG78.pep Hpt  46-132 1411 CGPG783.pep RRM_1:RRM_2 288-354::682-778 1412 CGPG7832.pep STT3  26-670 1413 CGPG7841.pep ECH::3HCDH_N::3HCDH 17-186::311- 490::492-585 1414 CGPG7845.pep LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1:: 23-64::97- LRR_1 119::121-143::145- 167::169-192::194- 216 1415 CGPG7847.pep Peptidase_C48  30-225 1417 CGPG7853.pep LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_ 142-164::166- 1::LRR_1 188::190-212::214- 235::258-280::282- 304::306-325 1418 CGPG7857.pep Response_reg::CCT 79-195::689-736 1420 CGPG7869.pep Acyltransferase 117-264 1421 CGPG7891.pep FMO-like  11-427 1422 CGPG7892.pep FMO-like  9-416 1423 CGPG7906.pep Skp1_POZ::Skp1 4-65::76-153 1424 CGPG7924.pep AAA 249-462 1428 CGPG7964.pep IQ::IQ 108-128::130-150 1429 CGPG7968.pep FMO-like  13-427 1431 CGPG7972.pep FAD_binding_3  5-372 1432 CGPG7982.pep Tetraspannin  4-241 1433 CGPG7985.pep BT1  57-469 1434 CGPG7993.pep F-box::LRR_2 27-73::278-304 1435 CGPG8.pep p450  39-503 1436 CGPG80.pep Pkinase  68-328 1437 CGPG8001.pep FMO-like  13-433 1438 CGPG8009.pep BT1  41-511 1440 CGPG8049.pep BT1  1-436 1441 CGPG806.pep Synaptobrevin 127-215 1442 CGPG8060.pep DUF829 161-425 1446 CGPG81.pep Pkinase  70-330 1452 CGPG8125.pep zf-C3HC4 46-86 1453 CGPG8134.pep DEK_C::SWIB::SWIB 3-57::197- 272::305-382 1455 CGPG8156.pep PCI 258-362 1456 CGPG8159.pep ACT::ACT 77-141::308-374 1458 CGPG8179.pep WD40::WD40 138-177::264-305 1459 CGPG8193.pep Ank::Ank 22-54::55-87 1460 CGPG8197.pep F-box  5-53 1461 CGPG8198.pep F-box::Kelch_2::Kelch_1::Kelch_2 74-119::174- 221::223-278::329- 369 1463 CGPG8211.pep F- 182-229::292- box::WD40::WD40::WD40::WD40::WD40:: 328::332-368::372- WD40 408::411-449::453- 538::542-578 1464 CGPG823.pep Ribosomal_S6e  1-129 1466 CGPG8238.pep PGI  49-537 1467 CGPG8260.pep Iso_dh  4-331 1468 CGPG8267.pep Pyridoxal_deC  34-383 1469 CGPG8268.pep NIR_SIR_ferr::NIR_SIR::NIR_SIR_ferr 62-131::164- 345::360-432 1470 CGPG8274.pep PK::PK_C 5-347::363-476 1471 CGPG8277.pep Rib_5-P_isom_A  55-229 1472 CGPG8279.pep F-box::Kelch_1::Kelch_1 22-69::124- 168::170-213 1475 CGPG8408.pep DUF641  60-192 1476 CGPG842.pep Redoxin  5-162 1477 CGPG8421.pep NOSIC::Nop 121-173::213-361 1478 CGPG8435.pep NHL::NHL 55-82::115-142 1479 CGPG8440.pep U-box::Arm::Arm::Arm::Arm 242-316::372- 413::455-495::496- 537::538-578 1480 CGPG8453.pep ACT::ACT::ACT::ACT 36-99::129- 201::265-332::343- 406 1481 CGPG8470.pep DUF89  18-357 1482 CGPG8479.pep F-box::Kelch_1::Kelch_1 31-78::124- 170::172-216 1483 CGPG8489.pep F-box::FBA_1 3-50::219-384 1484 CGPG8498.pep Fcf1  87-185 1485 CGPG85.pep Aa_trans  19-454 1486 CGPG8501.pep PPR::PPR::PPR::PPR::PPR::PPR 149-183::189- 223::224-258::259- 292::330-364::401- 435 1487 CGPG8507.pep DUF588  31-185 1488 CGPG8509.pep Pro_isomerase  80-233 1490 CGPG8517.pep B_lectin::S_locus_glycop::PAN_2 84-197::211- 339::356-422 1492 CGPG852.pep Ribosomal_S5::Ribosomal_S5_C 94-160::177-250 1498 CGPG8567.pep TB2_DP1_HVA22  3-98 1499 CGPG8580.pep Caleosin  22-195 1501 CGPG8590.pep DUF579  42-289 1503 CGPG8594.pep DUF584  1-139 1504 CGPG8606.pep Exo_endo_phos  56-327 1505 CGPG8628.pep DUF584  32-203 1507 CGPG8654.pep PPR::PPR 73-107::141-175 1508 CGPG8668.pep TATA_RF  1-200 1511 CGPG8702.pep RPE65  50-622 1514 CGPG8748.pep AAA 201-357 1516 CGPG8770.pep DUF543  1-73 1517 CGPG8777.pep DUF569::DUF569 1-144::227-368 1519 CGPG8786.pep DUF260  13-113 1520 CGPG8792.pep Abhydrolase_3  75-290 1521 CGPG8801.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR 110-144::145- 179::181-215::216- 250::251-285::286- 320::321-355 1522 CGPG8809.pep Ribosomal_L12 141-208 1523 CGPG8840.pep CLP_protease 145-289 1524 CGPG8850.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR:: 189-223::224- PPR::PPR 258::297-331::332- 366::367-401::402- 436::437-470::471- 505::506-540::542- 576 1525 CGPG8870.pep Fructosamin_kin  54-339 1526 CGPG8871.pep DUF59  36-115 1527 CGPG8872.pep RRM_1::RRM_1::RRM_1 138-205::214- 288::308-378 1528 CGPG8876.pep SFT2  43-162 1529 CGPG8902.pep RNA_pol_I_A49  31-415 1530 CGPG8904.pep G-alpha 103-447 1531 CGPG8907.pep DnaJ::zf-C2H2 4-67::338-362 1532 CGPG8914.pep Whi5 181-205 1533 CGPG8931.pep eIF3_subunit  1-231 1534 CGPG8933.pep MACPF 126-322 1535 CGPG8935.pep Pkinase  33-324 1536 CGPG8938.pep Pkinase  71-348 1537 CGPG8944.pep PH  31-134 1538 CGPG895.pep DUF231 251-427 1540 CGPG8961.pep Dus  59-392 1541 CGPG8963.pep Pkinase 319-612 1542 CGPG898.pep DUF231 276-448 1543 CGPG8993.pep AAA::Rep_fac_C 44-226::237-326 1544 CGPG8994.pep Brix  86-262 1545 CGPG8995.pep Porin_3  54-326 1546 CGPG90.pep MFS_1  68-427 1547 CGPG900.pep DUF231 241-420 1548 CGPG9002.pep CTP_transf_1  51-382 1549 CGPG9009.pep Alg6_Alg8  22-514 1550 CGPG9011.pep OTCace_N::OTCace 70-212::216-369 1551 CGPG9012.pep FolB  16-129 1552 CGPG9017.pep DMRL_synthase  70-213 1553 CGPG9025.pep Glyco_transf_29 105-355 1554 CGPG9026.pep Adap_comp_sub 160-428 1555 CGPG9032.pep RNase_PH::RNase_PH_C 33-165::194-262 1556 CGPG9040.pep Sec1  35-592 1557 CGPG9044.pep Syntaxin::SNARE 57-163::256-318 1558 CGPG9048.pep RNase_PH  15-135 1559 CGPG9049.pep Glycos_transf_1 244-442 1560 CGPG9058.pep RNA_pol_N  1-60 1561 CGPG906.pep PPR::PPR 210-244::245-279 1562 CGPG9070.pep ATP-synt_C::ATP-synt_C 20-85::104-169 1564 CGPG9084.pep GH::EB1 15-116::209-255 1566 CGPG9098.pep DUF6::DUF6 32-165::208-337 1567 CGPG9099.pep Rick_17 kDa_Anti  66-110 1568 CGPG9110.pep RALF  53-118 1569 CGPG9119.pep PTR2 115-504 1570 CGPG9125.pep ThiF  98-233 1571 CGPG913.pep PPR::PPR::PPR::PPR::PPR::PPR 86-120::188- 222::223-257::289- 323::325-358::361- 395 1574 CGPG9164.pep DHBP_synthase::GTP_cyclohydro2 5-202::207-377 1575 CGPG9172.pep Sec61_beta 32-77 1577 CGPG9185.pep DUF423  10-115 1578 CGPG9187.pep Pkinase  12-263 1579 CGPG9190.pep DREPP  2-203 1580 CGPG9193.pep GATase::GMP_synt_C 11-196::432-524 1581 CGPG9195.pep DUF1279 91-193 1582 CGPG9203.pep Na_H_Exchanger::TrkA_C 13-391::418-486 1583 CGPG9209.pep GATase::GMP_synt_C 9-197::423-515 1585 CGPG9210.pep Na_H_Exchanger::TrkA_N 10-376::402-517 1586 CGPG9211.pep NTP_transferase::MannoseP_isomer 7-296::307-473 1587 CGPG9212.pep ATP-synt_ab_N::ATP-synt_ab 22-87::143-353 1588 CGPG9216.pep DHBP_synthase::GTP_cyclohydro2 10-206::211-379 1589 CGPG9226.pep Carboxyl_trans  40-541 1590 CGPG9252.pep CDC48_N::AAA::AAA 28-114::245- 429::518-705 1592 CGPG9289.pep LSM 10-75 1593 CGPG9298.pep p450  41-516 1594 CGPG9299.pep ThiF  82-227 1597 CGPG9316.pep ATP-grasp_2::Ligase_CoA 34-242::285-421 1598 CGPG9317.pep DUF163  43-196 1599 CGPG9318.pep Aldo_ket_red  20-285 1600 CGPG9324.pep Pkinase 158-706 1601 CGPG9357.pep Raffinose_syn  7-757 1602 CGPG965.pep Hexapep::Hexapep::Hexapep::Hexapep 70-87::119- 136::142-159::160- 177 1603 CGPG970.pep NPH3 206-441 1604 CGPG982.pep p450  29-495 1605 CGPG994.pep adh_short  50-218 1606 CGPG996.pep DUF866  1-167

TABLE 21 PEP Seq ID No. Construct ID Pfam domain name Begin Stop score E-value 806 CGPG1023.pep Na_Ca_ex 104 255 94.2 4.10E−25 806 CGPG1023.pep Na_Ca_ex 299 432 128.4 2.10E−35 807 CGPG1038.pep DUF1475 1 256 709.5  2.40E−210 812 CGPG1113.pep DUF1350 49 370 64.5 3.50E−16 814 CGPG1163.pep DSPc 49 182 103 9.00E−28 817 CGPG1205.pep Arm 94 134 37.2 5.90E−08 817 CGPG1205.pep Arm 135 175 32.9 1.10E−06 817 CGPG1205.pep Arm 176 216 31.7 2.60E−06 817 CGPG1205.pep Arm 258 298 18.8 0.02   818 CGPG1207.pep NifU_N 26 105 78.3 2.60E−20 820 CGPG1223.pep ATP_bind_1 7 250 425.9  5.70E−125 821 CGPG1250.pep DUF822 12 160 323.6 3.70E−94 824 CGPG1319.pep DUF599 10 233 464.2  1.70E−136 826 CGPG1329.pep Cullin 29 631 966.3  1.20E−287 827 CGPG133.pep Cyclin_N 168 293 232.6 9.20E−67 827 CGPG133.pep Cyclin_C 295 422 170.5 4.50E−48 828 CGPG1332.pep Cullin 12 646 709.1  3.20E−210 829 CGPG1343.pep LRR_1 389 412 9.2 6     830 CGPG1348.pep Lectin_legB 27 248 295 1.40E−85 830 CGPG1348.pep Pkinase 334 604 170.2 5.30E−48 830 CGPG1348.pep Pkinase_Tyr 334 604 134.8 2.50E−37 831 CGPG1349.pep B_lectin 65 171 95.8 1.30E−25 831 CGPG1349.pep S_locus_glycop 180 312 105 2.40E−28 831 CGPG1349.pep PAN_1 327 404 38.5 2.40E−08 831 CGPG1349.pep Pkinase 484 731 167.1 4.70E−47 831 CGPG1349.pep Pkinase_Tyr 484 731 89.6 1.00E−23 832 CGPG1373.pep Pkinase 12 291 356.7  3.80E−104 833 CGPG1377.pep Pkinase 4 258 247.3 3.30E−71 834 CGPG1412.pep TPP_enzyme_N 45 221 286.5 5.40E−83 834 CGPG1412.pep TPP_enzyme_M 243 376 82.9 1.00E−21 834 CGPG1412.pep TPP_enzyme_C 431 578 35 3.50E−09 835 CGPG1421.pep Biotin_lipoyl 76 149 85.1 2.30E−22 835 CGPG1421.pep E3_binding 180 218 58.5 2.20E−14 835 CGPG1421.pep 2-oxoacid_dh 249 480 358.5  1.10E−104 836 CGPG1426.pep Aminotran_1_2 48 432 525  8.50E−155 837 CGPG1433.pep HI0933_like 44 365 −247.2 0.002  837 CGPG1433.pep GIDA 45 369 −206 0.00022 837 CGPG1433.pep Pyr_redox_2 45 359 241.5 1.90E−69 837 CGPG1433.pep Pyr_redox 216 313 115.7 1.40E−31 837 CGPG1433.pep Pyr_redox_dim 388 497 213.1 6.50E−61 838 CGPG1453.pep malic 171 360 412.3  7.10E−121 838 CGPG1453.pep Malic_M 362 615 468.8  7.10E−138 839 CGPG1454.pep Ribul_P_3_epim 7 207 331.5 1.50E−96 840 CGPG1463.pep Alpha-amylase 26 361 224.3 2.80E−64 840 CGPG1463.pep Alpha-amyl_C2 362 422 132.9 9.40E−37 841 CGPG1464.pep Glycolytic 11 358 852.5  2.20E−253 842 CGPG1471.pep IF4E 1 198 287.7 2.20E−83 843 CGPG1481.pep Pkinase 4 260 292.7 7.40E−85 844 CGPG1499.pep PPDK_N 85 445 654.8  6.90E−194 844 CGPG1499.pep PEP-utilizers 496 586 165.9 1.10E−46 844 CGPG1499.pep PEP-utilizers_C 598 955 688.7  4.30E−204 845 CGPG150.pep p450 30 507 128 2.80E−35 846 CGPG1536.pep CRAL_TRIO_N 73 142 46.4 1.00E−10 846 CGPG1536.pep CRAL_TRIO 159 345 145.1 2.00E−40 847 CGPG1539.pep UPF0139 8 107 215.9 9.60E−62 848 CGPG155.pep GlutR_N 100 251 288.2 1.70E−83 848 CGPG155.pep Shikimate_DH 255 407 208.3 1.80E−59 848 CGPG155.pep GlutR_dimer 420 526 180.6 4.10E−51 849 CGPG1583.pep PLAC8 88 187 176.8 5.40E−50 850 CGPG1588.pep PLAC8 75 214 156.3 8.30E−44 851 CGPG16.pep MIP 14 235 396.7  3.60E−116 852 CGPG1609.pep MMR_HSR1 54 190 118.9 1.50E−32 852 CGPG1609.pep DUF933 337 420 205.4 1.40E−58 853 CGPG1629.pep WD40 262 301 31.1 4.20E−06 853 CGPG1629.pep WD40 307 346 36 1.30E−07 853 CGPG1629.pep WD40 356 395 41.3 3.50E−09 854 CGPG1637.pep DUF220 163 262 148.5 1.80E−41 855 CGPG1653.pep TBC 200 415 −15 1.60E−06 856 CGPG1658.pep Nodulin-like 14 260 516.4  3.30E−152 857 CGPG1663.pep MFS_1 22 387 26.3 0.00011 857 CGPG1663.pep BT1 30 441 633.5  1.90E−187 858 CGPG1682.pep OPT 62 685 688.8  4.20E−204 859 CGPG1701.pep Glyco_transf_8 76 299 13.5 1.90E−07 861 CGPG1724.pep Per1 63 334 669.6  2.50E−198 862 CGPG1726.pep DUF607 111 291 388.6  9.80E−114 863 CGPG1736.pep Usp 1 148 64.9 2.70E−16 864 CGPG1741.pep mTERF 279 627 84.1 4.40E−22 865 CGPG1783.pep PB1 42 132 85 2.40E−22 866 CGPG1790.pep PB1 59 153 109.6 9.20E−30 868 CGPG1845.pep TFIID-18 kDa 29 119 145.5 1.50E−40 869 CGPG1855.pep CAF1 3 227 330.9 2.30E−96 870 CGPG1870.pep Pkinase 406 572 74.8 2.90E−19 871 CGPG1879.pep Pkinase 21 277 357.5  2.30E−104 871 CGPG1879.pep Pkinase_Tyr 21 275 88.2 2.60E−23 871 CGPG1879.pep NAF 303 364 98.7 1.80E−26 872 CGPG1886.pep Pkinase 26 325 337.3 2.70E−98 873 CGPG1903.pep F-box 320 367 41 4.30E−09 874 CGPG1905.pep F-box 4 51 41.7 2.60E−09 874 CGPG1905.pep Kelch_2 104 150 27.4 5.30E−05 874 CGPG1905.pep Kelch_2 255 306 41.6 2.80E−09 875 CGPG1914.pep F-box 42 89 39.8 9.50E−09 875 CGPG1914.pep Kelch_2 170 215 26.3 0.00011 875 CGPG1914.pep Kelch_1 170 215 52.2 1.80E−12 875 CGPG1914.pep Kelch_2 217 266 31.3 3.60E−06 875 CGPG1914.pep Kelch_1 217 266 59.1 1.50E−14 876 CGPG193.pep WD40 167 205 28.5 2.40E−05 876 CGPG193.pep WD40 268 307 24.4 0.00041 876 CGPG193.pep WD40 318 355 25.1 0.00026 876 CGPG193.pep WD40 363 401 39.3 1.40E−08 877 CGPG1939.pep F-box 66 113 36.2 1.20E−07 877 CGPG1939.pep WD40 152 190 26.2 0.00012 877 CGPG1939.pep WD40 247 283 33.6 7.10E−07 877 CGPG1939.pep WD40 325 364 22.9 0.0012  878 CGPG1949.pep YDG_SRA 360 519 403.5  3.10E−118 878 CGPG1949.pep Pre-SET 543 639 156.7 6.30E−44 878 CGPG1949.pep SET 641 771 178.4 1.80E−50 879 CGPG1959.pep PHD 34 82 54.3 4.30E−13 879 CGPG1959.pep SET 208 344 105.1 2.20E−28 880 CGPG197.pep p450 40 481 169.2 1.10E−47 882 CGPG1981.pep MT-A70 476 636 321.4 1.70E−93 883 CGPG1999.pep Nfu_N 78 193 145 2.10E−40 883 CGPG1999.pep NifU 221 291 121.1 3.30E−33 884 CGPG2.pep p450 71 531 324.3 2.20E−94 885 CGPG2006.pep RCC1 32 82 31.3 3.60E−06 885 CGPG2006.pep RCC1 138 187 40 8.30E−09 885 CGPG2006.pep RCC1 190 239 33 1.10E−06 885 CGPG2006.pep RCC1 294 343 42.8 1.20E−09 886 CGPG2010.pep Aminotran_5 74 448 681.1  8.90E−202 886 CGPG2010.pep Beta_elim_lyase 77 389 −107.3 0.0021  887 CGPG2011.pep X8 128 209 153.5 5.60E−43 888 CGPG2014.pep Pkinase 28 282 339.2 7.00E−99 888 CGPG2014.pep NAF 341 398 86.9 6.70E−23 889 CGPG2023.pep Zip 48 352 371  1.90E−108 890 CGPG2026.pep Pkinase 38 324 328.9 9.40E−96 892 CGPG2064.pep Cenp-O 123 201 107.6 3.80E−29 894 CGPG2077.pep NAC 88 147 81.6 2.50E−21 894 CGPG2077.pep UBA 195 232 29.8 1.00E−05 895 CGPG2095.pep AARP2CN 228 309 121.6 2.30E−33 895 CGPG2095.pep DUF663 483 780 615.9  3.60E−182 896 CGPG2105.pep Pkinase 102 404 274.6 2.00E−79 896 CGPG2105.pep Pkinase_C 422 471 39.6 1.10E−08 897 CGPG2108.pep Response_reg 64 180 86.8 6.80E−23 897 CGPG2108.pep CCT 442 484 65 2.50E−16 898 CGPG2111.pep polyprenyl_synt 74 324 156.4 7.70E−44 899 CGPG2124.pep UIM 139 156 20.6 0.0057  899 CGPG2124.pep efhand 220 248 35.7 1.70E−07 900 CGPG2125.pep Glutaredoxin 44 110 40.7 5.10E−09 903 CGPG2134.pep ATP-synt_G 8 122 170.2 5.30E−48 904 CGPG2139.pep DUF1517 94 391 709.7  2.10E−210 905 CGPG2140.pep PhzC-PhzF 6 282 506.2  3.90E−149 907 CGPG2163.pep Cupin_1 5 157 105.9 1.20E−28 907 CGPG2163.pep Cupin_1 190 339 83.5 6.80E−22 908 CGPG2165.pep ClpS 76 152 131.5 2.40E−36 910 CGPG2218.pep Spc97_Spc98 67 555 750.6  1.10E−222 912 CGPG2225.pep EMP24_GP25L 52 116 55.6 1.80E−13 913 CGPG2229.pep Subtilisin_N 30 106 89.6 9.70E−24 913 CGPG2229.pep Peptidase_S8 119 600 52.4 1.60E−12 913 CGPG2229.pep PA 362 461 112 1.80E−30 915 CGPG2254.pep Ribosomal_L7Ae 20 114 110.3 5.80E−30 916 CGPG2268.pep CBS 66 188 107.9 3.00E−29 917 CGPG227.pep p450 37 494 364.2  2.20E−106 918 CGPG2312.pep UPF0061 75 571 361.8  1.20E−105 919 CGPG2315.pep SIP1 286 514 516.5  3.10E−152 920 CGPG2316.pep PTPA 98 396 696.6  1.80E−206 922 CGPG235.pep p450 74 510 203.2 6.10E−58 923 CGPG2358.pep Branch 54 278 425.3  8.70E−125 925 CGPG2361.pep Metallophos 9 231 49.7 1.00E−11 926 CGPG2365.pep Epimerase 3 211 −25.8 3.00E−05 927 CGPG2372.pep Pribosyltran 29 169 147.9 2.70E−41 928 CGPG2374.pep Aminotran_5 8 370 −92.6 4.20E−07 929 CGPG2377.pep DAO 69 466 243.4 5.00E−70 929 CGPG2377.pep FAD_binding_2 69 457 −124 0.0024  930 CGPG2387.pep H_PPase 1 239 −188.8 6.80E−17 931 CGPG2389.pep Carb_anhydrase 52 275 117.4 4.30E−32 932 CGPG2395.pep AA_permease 89 526 −4.2 1.30E−05 934 CGPG2409.pep DUF862 17 154 252.5 8.90E−73 935 CGPG2410.pep GST_N 5 79 68.9 1.70E−17 935 CGPG2410.pep GST_C 101 204 30.1 8.30E−06 937 CGPG2416.pep Hin1 97 235 198.2 2.10E−56 938 CGPG2441.pep Sina 5 205 188 2.30E−53 939 CGPG2450.pep adh_short 112 282 −38.2 0.004  939 CGPG2450.pep Epimerase 114 371 191.5 2.10E−54 939 CGPG2450.pep 3Beta_HSD 115 402 −72.8 1.60E−05 939 CGPG2450.pep NAD_binding_4 116 342 −62.5 9.90E−05 940 CGPG2451.pep RALF 57 129 123.9 4.80E−34 941 CGPG2492.pep Pribosyltran 80 216 144.1 3.80E−40 942 CGPG2495.pep ADH_N 25 134 143.2 7.40E−40 942 CGPG2495.pep ADH_zinc_N 165 307 138 2.60E−38 943 CGPG2506.pep PfkB 5 289 140.3 5.30E−39 944 CGPG2515.pep TIM 5 244 446  5.10E−131 945 CGPG2531.pep Redoxin 4 160 43.7 6.60E−10 945 CGPG2531.pep AhpC-TSA 5 138 178.9 1.30E−50 946 CGPG2581.pep SeIR 12 133 289.3 7.50E−84 947 CGPG2584.pep zf-Tim10_DDP 22 86 115.1 2.00E−31 948 CGPG2592.pep TFIID_30 kDa 30 80 135.9 1.10E−37 949 CGPG2612.pep RRM_1 65 132 43 1.10E−09 949 CGPG2612.pep RRM_1 150 225 83.9 5.30E−22 949 CGPG2612.pep RRM_1 275 343 53.1 9.50E−13 950 CGPG2660.pep B3 17 115 77.8 3.60E−20 950 CGPG2660.pep B3 211 301 61.4 3.10E−15 951 CGPG2663.pep NTF2 15 131 168.8 1.50E−47 951 CGPG2663.pep RRM_1 295 365 45.3 2.10E−10 952 CGPG2679.pep ACBP 104 190 54.4 3.80E−13 952 CGPG2679.pep Ank 265 297 49.7 1.00E−11 952 CGPG2679.pep Ank 298 330 35.5 2.00E−07 953 CGPG2696.pep zf-C3HC4 177 218 43.9 5.70E−10 954 CGPG2772.pep Mov34 6 136 111.9 1.90E−30 955 CGPG2773.pep Asp 161 498 −73.6 3.00E−09 956 CGPG281.pep TLC 91 574 1046.6 0     957 CGPG2846.pep Aldo_ket_red 49 365 248 2.00E−71 958 CGPG2852.pep Glyoxalase 9 132 37.4 5.20E−08 960 CGPG2870.pep zf-CCCH 111 137 49.3 1.30E−11 960 CGPG2870.pep zf-CCCH 159 185 34.6 3.60E−07 960 CGPG2870.pep zf-CCCH 205 231 49.5 1.20E−11 960 CGPG2870.pep zf-CCCH 347 373 29.9 9.60E−06 960 CGPG2870.pep zf-CCCH 393 419 42.5 1.50E−09 961 CGPG2877.pep LAG1 96 307 430.8  1.90E−126 962 CGPG289.pep Cellulose_synt 243 1060 2161.1 0     963 CGPG2924.pep zf-C3HC4 138 179 33.3 9.10E−07 964 CGPG2947.pep Acetyltransf_1 265 343 50.6 5.60E−12 964 CGPG2947.pep Bromodomain 460 548 122.2 1.50E−33 965 CGPG2963.pep C1_3 80 108 35.7 1.60E−07 965 CGPG2963.pep C1_2 81 108 37.1 6.10E−08 965 CGPG2963.pep C1_1 122 172 14.3 0.00058 965 CGPG2963.pep C1_3 136 164 36.3 1.10E−07 965 CGPG2963.pep C1_3 194 223 27.2 6.10E−05 965 CGPG2963.pep C1_2 305 335 40.5 5.90E−09 965 CGPG2963.pep C1_3 391 420 40.1 8.20E−09 965 CGPG2963.pep C1_3 494 522 25.6 0.00018 965 CGPG2963.pep C1_3 551 581 27.5 5.00E−05 965 CGPG2963.pep C1_2 552 581 47.9 3.50E−11 966 CGPG2987.pep SRF-TF 11 66 24.4 0.00041 968 CGPG3045.pep Pkinase 82 356 192 1.50E−54 968 CGPG3045.pep Pkinase_Tyr 82 356 254 3.20E−73 969 CGPG3046.pep AAA 121 305 245.7 1.00E−70 970 CGPG3060.pep p450 67 528 268 1.90E−77 971 CGPG3075.pep Auxin_inducible 7 106 121 3.50E−33 972 CGPG310.pep Cyclin_N 18 143 31.8 1.80E−07 973 CGPG3103.pep PPR 14 48 10.8 0.4   973 CGPG3103.pep PPR 49 83 37.5 4.80E−08 973 CGPG3103.pep PPR 84 118 38.8 1.90E−08 973 CGPG3103.pep PPR 119 153 11.8 0.31   973 CGPG3103.pep PPR 155 188 27.6 4.50E−05 973 CGPG3103.pep PPR 189 223 34.8 3.20E−07 973 CGPG3103.pep PPR 224 258 36.8 7.80E−08 973 CGPG3103.pep PPR 259 293 7.7 0.95   973 CGPG3103.pep PPR 295 329 39.7 1.10E−08 973 CGPG3103.pep PPR 330 364 12.6 0.25   973 CGPG3103.pep PPR 365 398 30.4 6.70E−06 974 CGPG315.pep p450 29 491 346.8  3.80E−101 976 CGPG3189.pep RRM_1 115 186 101.9 2.00E−27 976 CGPG3189.pep RRM_1 209 280 104.9 2.40E−28 977 CGPG3204.pep KH_1 45 104 53.4 7.60E−13 977 CGPG3204.pep KH_1 151 221 58.6 2.20E−14 977 CGPG3204.pep KH_1 318 381 44.6 3.60E−10 977 CGPG3204.pep KH_2 318 365 11.3 0.019  977 CGPG3204.pep KH_1 400 467 63.4 7.50E−16 977 CGPG3204.pep KH_1 575 637 53.3 8.70E−13 978 CGPG3208.pep MATH 26 153 47.1 6.00E−11 978 CGPG3208.pep MATH 180 302 18.3 0.0015  979 CGPG3219.pep 2OG-FeII_Oxy 220 320 161.1 2.90E−45 980 CGPG3233.pep PPR 160 194 21.8 0.0026  980 CGPG3233.pep PPR 195 229 9.6 0.56   980 CGPG3233.pep PPR 231 265 24.1 0.00052 980 CGPG3233.pep PPR 266 300 40.7 5.10E−09 980 CGPG3233.pep PPR 301 335 44 5.30E−10 980 CGPG3233.pep PPR 336 370 45.3 2.20E−10 980 CGPG3233.pep PPR 371 405 44.7 3.30E−10 980 CGPG3233.pep PPR 406 440 7.4 1     981 CGPG3263.pep Tryp_alpha_amyl 28 104 36.6 8.90E−08 982 CGPG3276.pep ECH 11 186 48.1 3.10E−11 984 CGPG3282.pep Steroid_dh 117 268 65.5 1.80E−16 985 CGPG3300.pep zf-CCHC 55 72 30.4 6.40E−06 985 CGPG3300.pep zf-CCHC 74 91 26.8 7.80E−05 985 CGPG3300.pep zf-CCHC 93 110 29.8 1.00E−05 985 CGPG3300.pep zf-CCHC 112 129 27.3 5.70E−05 985 CGPG3300.pep zf-CCHC 138 155 23.8 0.00038 985 CGPG3300.pep zf-CCHC 157 174 24.9 0.00026 985 CGPG3300.pep zf-CCHC 229 246 26.5 9.70E−05 986 CGPG3318.pep Peptidase_C14 3 416 273.4 4.50E−79 987 CGPG3319.pep AP2 28 79 61.2 3.40E−15 988 CGPG3326.pep zf-C3HC4 259 299 36.8 7.90E−08 989 CGPG333.pep PTS_2-RNA 48 239 409.9  3.80E−120 990 CGPG3338.pep Alba 17 87 114.8 2.50E−31 991 CGPG334.pep Mov34 20 128 65.2 2.20E−16 992 CGPG3374.pep peroxidase 42 286 426.2  4.60E−125 993 CGPG3402.pep Dimerisation 30 89 93.1 8.60E−25 993 CGPG3402.pep Methyltransf_2 99 342 287.6 2.40E−83 995 CGPG3413.pep WD40 168 207 41.5 3.10E−09 995 CGPG3413.pep U3_snoRNA_C 377 523 212.3 1.10E−60 996 CGPG3422.pep WD40 241 279 41.2 3.70E−09 996 CGPG3422.pep WD40 387 425 35.3 2.20E−07 996 CGPG3422.pep WD40 519 559 21.9 0.0024  997 CGPG3436.pep DUF6 17 144 33.8 6.40E−07 997 CGPG3436.pep DUF6 198 327 50.4 6.10E−12 998 CGPG3539.pep Mito_carr 11 105 84.6 3.10E−22 998 CGPG3539.pep Mito_carr 113 209 115.7 1.40E−31 998 CGPG3539.pep Mito_carr 214 303 102.2 1.60E−27 999 CGPG3550.pep FAE1_CUT1_RppA 81 370 700.9  9.60E−208 999 CGPG3550.pep Chal_sti_synt_C 327 470 2.6 0.0011  999 CGPG3550.pep ACP_syn_III_C 384 468 21.5 8.90E−08 1000 CGPG3551.pep Pkinase 9 273 145.9 1.10E−40 1001 CGPG3552.pep Aldedh 23 441 176.5 6.90E−50 1002 CGPG3572.pep FA_hydroxylase 112 225 133.2 7.50E−37 1004 CGPG3599.pep DUF579 51 289 588.5  6.70E−174 1008 CGPG364.pep zf-C3HC4 97 137 51 4.30E−12 1010 CGPG3679.pep malic 36 179 249.1 9.50E−72 1010 CGPG3679.pep Malic_M 181 418 426.3  4.30E−125 1010 CGPG3679.pep PTA_PTB 446 768 457.7  1.60E−134 1011 CGPG3686.pep Gp_dh_N 2 150 334.5 1.80E−97 1011 CGPG3686.pep Gp_dh_C 155 312 388.4  1.10E−113 1012 CGPG3694.pep LRRNT_2 38 78 64.2 4.40E−16 1012 CGPG3694.pep LRR_1 106 128 11.7 2.1   1012 CGPG3694.pep LRR_1 130 152 14.2 0.48   1012 CGPG3694.pep LRR_1 154 176 16.7 0.089  1012 CGPG3694.pep LRR_1 178 201 11.7 2.1   1012 CGPG3694.pep Pkinase 312 583 104.7 2.80E−28 1012 CGPG3694.pep Pkinase_Tyr 312 583 110.8 4.20E−30 1013 CGPG3696.pep MMR_HSR1 136 257 120.2 5.90E−33 1014 CGPG3698.pep WD40 104 142 31.6 2.80E−06 1014 CGPG3698.pep WD40 234 272 22.5 0.0016  1015 CGPG3699.pep adh_short 19 187 111.6 2.30E−30 1015 CGPG3699.pep KR 19 203 −54.2 0.00034 1016 CGPG3702.pep SAM_2 227 293 48.9 1.80E−11 1016 CGPG3702.pep SAM_1 228 291 52.7 1.30E−12 1017 CGPG3703.pep ENOD93 25 103 190.1 5.50E−54 1018 CGPG3707.pep Pkinase 42 333 296.2 6.30E−86 1019 CGPG3710.pep VQ 118 148 45.7 1.60E−10 1020 CGPG3730.pep DUF167 140 216 99.7 9.10E−27 1021 CGPG3731.pep DUF616 194 508 769.9  1.60E−228 1022 CGPG3734.pep PRK 46 233 177.1 4.40E−50 1022 CGPG3734.pep Pribosyltran 280 425 5.8 0.00083 1023 CGPG3745.pep RRM_1 386 455 66.7 7.80E−17 1023 CGPG3745.pep RRM_1 481 553 49.6 1.10E−11 1024 CGPG3764.pep Response_reg 20 145 67.1 5.90E−17 1026 CGPG3851.pep SH3_1 284 338 42.4 1.60E−09 1026 CGPG3851.pep SH3_2 285 338 30.1 8.10E−06 1027 CGPG3911.pep Aldedh 104 587 526.9  2.20E−155 1028 CGPG3948.pep NAP 50 295 467.9  1.30E−137 1031 CGPG3996.pep Inositol_P 6 267 363.1  4.60E−106 1032 CGPG4006.pep ENT 1 74 140.3 5.60E−39 1033 CGPG4025.pep SQS_PSY 44 331 455.8  5.80E−134 1034 CGPG4028.pep Transket_pyr 398 565 233 6.90E−67 1034 CGPG4028.pep Transketolase_C 579 702 152.2 1.40E−42 1035 CGPG403.pep Pkinase 78 336 354.1  2.40E−103 1036 CGPG4041.pep DEAD 141 315 219 1.10E−62 1036 CGPG4041.pep Helicase_C 386 462 120.8 4.10E−33 1037 CGPG4078.pep GST_C 180 283 23.1 0.00038 1038 CGPG4079.pep RRS1 1 178 271.1 2.30E−78 1041 CGPG4104.pep LRRNT_2 30 67 33.1 1.00E−06 1041 CGPG4104.pep LRR_1 95 117 11.4 2.3   1041 CGPG4104.pep LRR_1 119 141 15.5 0.21   1041 CGPG4104.pep LRR_1 143 165 12.1 1.8   1041 CGPG4104.pep LRR_1 167 188 16.1 0.13   1041 CGPG4104.pep Pkinase 367 633 99.2 1.30E−26 1042 CGPG4127.pep Hydrolase 43 239 93.3 7.50E−25 1043 CGPG4135.pep Pkinase 118 376 357.9  1.70E−104 1043 CGPG4135.pep efhand 423 451 41.5 3.10E−09 1043 CGPG4135.pep efhand 459 487 24.8 0.00033 1043 CGPG4135.pep efhand 495 523 30.6 5.70E−06 1043 CGPG4135.pep efhand 529 557 40.3 7.00E−09 1044 CGPG4161.pep Methyltransf_11 56 159 48 3.30E−11 1044 CGPG4161.pep Methyltransf_12 56 157 31.8 2.40E−06 1045 CGPG4180.pep GHMP_kinases_N 152 219 64.2 4.40E−16 1045 CGPG4180.pep GHMP_kinases_C 382 466 58.4 2.50E−14 1046 CGPG4191.pep Bombesin 163 176 14.8 0.16   1047 CGPG4199.pep Copine 117 265 295.3 1.20E−85 1047 CGPG4199.pep zf-C3HC4 385 417 16.2 0.0013  1048 CGPG4241.pep GASA 3 99 179.9 6.40E−51 1049 CGPG427.pep Pkinase 8 262 210 5.80E−60 1049 CGPG427.pep Pkinase_Tyr 8 262 248 2.10E−71 1050 CGPG4273.pep dsrm 2 68 70 7.70E−18 1050 CGPG4273.pep dsrm 88 153 66.9 6.90E−17 1051 CGPG4301.pep 2OG-FeII_Oxy 151 253 97 6.00E−26 1052 CGPG4303.pep Rhodanese 13 114 64.9 2.70E−16 1053 CGPG4313.pep G6PD_N 94 273 322.4 8.50E−94 1053 CGPG4313.pep G6PD_C 276 573 522.2  6.00E−154 1054 CGPG4314.pep AWPM-19 15 156 335.5 9.50E−98 1055 CGPG4329.pep AA_kinase 86 324 201.9 1.60E−57 1056 CGPG4330.pep PALP 53 341 418.6  9.40E−123 1057 CGPG4338.pep Proteasome 21 217 157.3 4.00E−44 1058 CGPG4341.pep Mito_carr 51 134 78 3.10E−20 1058 CGPG4341.pep Mito_carr 158 246 81.5 2.80E−21 1058 CGPG4341.pep Mito_carr 252 343 82.8 1.10E−21 1061 CGPG4386.pep GHMP_kinases_N 113 171 55.4 1.90E−13 1061 CGPG4386.pep GHMP_kinases_C 245 338 29.5 1.20E−05 1062 CGPG4394.pep p450 39 503 389.1  7.00E−114 1063 CGPG4396.pep p450 39 504 355.6  8.20E−104 1064 CGPG4400.pep p450 32 474 146.7 6.70E−41 1065 CGPG4401.pep p450 47 511 383.1  4.60E−112 1066 CGPG441.pep Chalcone 14 225 498.4  8.60E−147 1067 CGPG4413.pep p450 32 547 286.5 5.20E−83 1068 CGPG4427.pep p450 57 530 225.1 1.60E−64 1069 CGPG4446.pep p450 43 504 275.6 1.00E−79 1070 CGPG4448.pep p450 32 486 332.3 8.70E−97 1071 CGPG4474.pep Band_7 33 212 136.8 5.90E−38 1072 CGPG4482.pep peroxidase 47 291 314.4 2.10E−91 1073 CGPG4511.pep VHS 36 166 58.2 2.80E−14 1073 CGPG4511.pep GAT 227 315 18.1 2.80E−05 1074 CGPG4517.pep Aldo_ket_red 5 292 460.6  2.10E−135 1075 CGPG4551.pep XS 30 148 250.2 4.60E−72 1075 CGPG4551.pep XH 418 557 251.6 1.70E−72 1077 CGPG4567.pep SRF-TF 3 53 85.4 1.80E−22 1078 CGPG4586.pep RRM_1 8 73 41.5 2.90E−09 1079 CGPG4600.pep zf-CCCH 13 39 35.4 2.00E−07 1079 CGPG4600.pep zf-CCCH 149 174 24.1 0.00053 1080 CGPG4631.pep C1_3 87 115 40.8 4.80E−09 1080 CGPG4631.pep C1_2 88 115 41.2 3.80E−09 1080 CGPG4631.pep C1_3 208 237 39.4 1.30E−08 1080 CGPG4631.pep C1_2 209 237 45.5 1.80E−10 1080 CGPG4631.pep C1_3 264 292 48.3 2.70E−11 1080 CGPG4631.pep C1_2 319 349 41.5 2.90E−09 1080 CGPG4631.pep C1_3 404 433 55.4 1.90E−13 1080 CGPG4631.pep C1_2 566 595 40.8 4.70E−09 1081 CGPG4642.pep Pyridoxal_deC 63 412 126.5 7.90E−35 1082 CGPG4645.pep Cu-oxidase_3 31 148 198.9 1.30E−56 1082 CGPG4645.pep Cu-oxidase 157 325 222.3 1.10E−63 1082 CGPG4645.pep Cu-oxidase_2 414 551 155.1 2.00E−43 1083 CGPG4646.pep efhand_like 27 105 109.6 9.60E−30 1083 CGPG4646.pep PI-PLC-X 108 251 143.6 5.60E−40 1083 CGPG4646.pep PI-PLC-Y 332 450 93.9 5.20E−25 1083 CGPG4646.pep C2 471 563 82.3 1.50E−21 1084 CGPG4649.pep SMP 14 72 102 1.90E−27 1084 CGPG4649.pep SMP 130 191 127.6 3.60E−35 1084 CGPG4649.pep SMP 195 256 62.7 1.30E−15 1085 CGPG4653.pep DUF1637 47 280 366.2  5.30E−107 1087 CGPG4668.pep SYF2 140 306 301.7 1.50E−87 1088 CGPG469.pep tRNA-synt_1c 213 518 428.8  7.70E−126 1088 CGPG469.pep tRNA-synt_1c_C 520 697 229.4 8.00E−66 1089 CGPG4708.pep Sulfate_transp 172 482 504.9  9.60E−149 1089 CGPG4708.pep STAS 505 623 142.8 9.80E−40 1090 CGPG4712.pep Mem_trans 9 565 715.3  4.30E−212 1091 CGPG4714.pep DUF231 248 423 336.8 3.80E−98 1092 CGPG4719.pep Response_reg 37 153 91.6 2.50E−24 1092 CGPG4719.pep CCT 417 461 85 2.40E−22 1093 CGPG473.pep Peptidase_M16 88 234 184 3.90E−52 1093 CGPG473.pep Peptidase_M16_C 239 423 161.3 2.70E−45 1094 CGPG4734.pep Auxin_inducible 19 119 55.4 1.90E−13 1095 CGPG4736.pep Pribosyltran 225 358 139.9 7.20E−39 1096 CGPG474.pep Pro_isomerase 6 172 426  5.20E−125 1102 CGPG4850.pep PMEI 25 174 138.8 1.60E−38 1103 CGPG4868.pep PsbW 1 133 333 5.40E−97 1104 CGPG4871.pep Tryp_alpha_amyl 52 133 98.3 2.30E−26 1105 CGPG488.pep Histone 19 92 110.5 5.00E−30 1105 CGPG488.pep CBFD_NFYB_HMF 25 89 20.6 0.002  1106 CGPG4908.pep WD40 16 54 22.1 0.002  1106 CGPG4908.pep WD40 63 101 22.2 0.002  1108 CGPG4921.pep WD40 202 241 26.8 7.90E−05 1108 CGPG4921.pep WD40 253 291 41.3 3.40E−09 1108 CGPG4921.pep WD40 295 333 33.5 7.40E−07 1108 CGPG4921.pep WD40 337 375 47.3 5.20E−11 1108 CGPG4921.pep WD40 472 510 25.7 0.00017 1109 CGPG4954.pep LRRNT_2 33 72 38.6 2.20E−08 1109 CGPG4954.pep LRR_1 76 98 9 6.5   1109 CGPG4954.pep LRR_1 100 122 12.7 1.4   1109 CGPG4954.pep LRR_1 124 145 8 10     1110 CGPG4956.pep Asp 141 482 −61.6 5.90E−10 1111 CGPG4959.pep adh_short 15 183 94.8 2.80E−25 1111 CGPG4959.pep KR 16 200 −64.6 0.0014  1112 CGPG4965.pep zf-A20 15 39 32.9 1.20E−06 1112 CGPG4965.pep zf-AN1 114 154 64.5 3.50E−16 1113 CGPG4970.pep GASA 1 108 225.3 1.40E−64 1114 CGPG4980.pep U-box 73 147 95.4 1.80E−25 1114 CGPG4980.pep Arm 246 287 20.1 0.0085  1114 CGPG4980.pep Arm 288 328 22.4 0.0017  1115 CGPG4982.pep F-box 2 49 42.8 1.20E−09 1115 CGPG4982.pep FBA_1 209 387 313.8 3.20E−91 1116 CGPG4985.pep CPSase_sm_chain 56 203 298.5 1.30E−86 1116 CGPG4985.pep GATase 245 422 238.5 1.50E−68 1117 CGPG4990.pep LRRNT_2 73 112 28.9 1.90E−05 1117 CGPG4990.pep LRR_1 139 161 13.9 0.59   1117 CGPG4990.pep LRR_1 163 183 13.6 0.73   1117 CGPG4990.pep LRR_1 187 206 13.9 0.62   1117 CGPG4990.pep LRR_1 210 232 8.2 9.1   1117 CGPG4990.pep LRR_1 306 328 9.8 4.6   1118 CGPG4991.pep PALP 164 473 254.7 2.00E−73 1119 CGPG5007.pep adh_short 21 192 65.9 1.30E−16 1119 CGPG5007.pep Epimerase 23 271 −42.4 0.00053 1120 CGPG5015.pep adh_short 13 126 −22.3 0.00036 1121 CGPG5026.pep adh_short 46 221 22.7 4.00E−07 1122 CGPG5029.pep adh_short 80 252 70.7 4.90E−18 1123 CGPG5046.pep LRRNT_2 30 70 51.2 3.60E−12 1123 CGPG5046.pep LRR_1 99 121 9.2 6     1123 CGPG5046.pep LRR_1 123 145 10.5 3.4   1123 CGPG5046.pep LRR_1 147 169 15.8 0.16   1123 CGPG5046.pep Pkinase_Tyr 306 573 109.4 1.10E−29 1123 CGPG5046.pep Pkinase 306 573 145.6 1.40E−40 1124 CGPG508.pep Na_sulph_symp 93 563 619  4.30E−183 1125 CGPG5103.pep C2 9 95 64.8 3.00E−16 1126 CGPG511.pep Rho_GDI 22 222 43.8 6.70E−12 1127 CGPG5121.pep efhand_like 30 113 41.4 3.20E−09 1127 CGPG5121.pep PI-PLC-X 116 258 140.7 4.20E−39 1127 CGPG5121.pep PI-PLC-Y 331 449 88.6 2.00E−23 1127 CGPG5121.pep C2 470 562 81.3 3.00E−21 1128 CGPG5126.pep peroxidase 54 303 312 1.10E−90 1129 CGPG5136.pep p450 35 500 88.4 2.30E−23 1130 CGPG5146.pep p450 45 501 209 1.10E−59 1131 CGPG5149.pep p450 31 478 306.7 4.40E−89 1132 CGPG5181.pep Pkinase 278 540 112.7 1.10E−30 1133 CGPG52.pep Sugar_tr 32 472 −75.6 5.00E−06 1134 CGPG5206.pep UDPG_MGDP_dh_N 2 200 331.6 1.40E−96 1134 CGPG5206.pep UDPG_MGDP_dh 209 306 189.1 1.10E−53 1134 CGPG5206.pep UDPG_MGDP_dh_C 328 452 183.7 4.70E−52 1136 CGPG5232.pep Pkinase 71 328 295.9 8.10E−86 1137 CGPG5239.pep Copine 136 284 331.7 1.30E−96 1138 CGPG5246.pep ABC_tran 94 285 132.8 9.70E−37 1138 CGPG5246.pep ABC_tran 406 571 146.2 9.10E−41 1139 CGPG525.pep CDP-OH_P_transf 138 277 132.1 1.60E−36 1140 CGPG5268.pep CDC50 65 368 681.3  7.50E−202 1141 CGPG5272.pep AA_permease 153 621 569.2  4.10E−168 1142 CGPG5333.pep MFS_1 55 468 76 1.30E−19 1142 CGPG5333.pep Sugar_tr 89 515 21.1 8.20E−10 1143 CGPG5338.pep RRM_1 8 77 90.6 5.10E−24 1143 CGPG5338.pep RRM_1 108 178 82.6 1.30E−21 1144 CGPG5341.pep F-box 33 79 31.7 2.60E−06 1145 CGPG5369.pep AA_kinase 83 366 213.4 5.30E−61 1145 CGPG5369.pep ACT 400 469 20.9 0.0047  1145 CGPG5369.pep ACT 477 539 9.7 0.71   1146 CGPG5372.pep SBF 142 322 125.7 1.30E−34 1147 CGPG5380.pep Tyr-DNA_phospho 137 581 1043.5 0     1148 CGPG5386.pep MOSC_N 4 132 245 1.70E−70 1148 CGPG5386.pep MOSC 138 296 66.5 8.80E−17 1149 CGPG5396.pep PALP 9 297 469.3  5.00E−138 1150 CGPG5397.pep PDT 128 307 347.9  1.70E−101 1151 CGPG5421.pep Pre-SET 119 267 14.7 2.20E−05 1151 CGPG5421.pep SET 269 414 151.3 2.60E−42 1152 CGPG5433.pep MtN3_slv 10 98 144.3 3.30E−40 1152 CGPG5433.pep MtN3_slv 132 218 145.4 1.50E−40 1153 CGPG5439.pep LANC_like 69 410 459.8  3.60E−135 1154 CGPG5453.pep Mito_carr 14 116 102 1.80E−27 1154 CGPG5453.pep Mito_carr 125 215 98.8 1.60E−26 1154 CGPG5453.pep Mito_carr 233 334 104 4.60E−28 1155 CGPG5456.pep Mito_carr 78 175 128.9 1.50E−35 1155 CGPG5456.pep Mito_carr 183 279 100.4 5.50E−27 1155 CGPG5456.pep Mito_carr 283 373 91.5 2.70E−24 1156 CGPG5483.pep PP2C 66 369 92.8 1.10E−24 1157 CGPG5492.pep FAE1_CUT1_RppA 61 358 683.7  1.40E−202 1157 CGPG5492.pep Chal_sti_synt_C 312 458 −1.1 0.0023  1157 CGPG5492.pep ACP_syn_III_C 372 456 4.3 5.30E−06 1158 CGPG5508.pep RCC1 310 359 23.9 0.00059 1158 CGPG5508.pep RCC1 413 462 39 1.70E−08 1158 CGPG5508.pep RCC1 478 526 32.5 1.50E−06 1158 CGPG5508.pep RCC1 582 630 28.9 1.80E−05 1158 CGPG5508.pep FYVE 633 701 44.7 3.30E−10 1158 CGPG5508.pep DZC 967 1002 74 4.80E−19 1159 CGPG5520.pep TFIID-31 kDa 19 152 319.5 6.10E−93 1160 CGPG5525.pep PRMT5 187 679 1145.5 0     1161 CGPG5526.pep Pkinase 8 295 335.7 8.20E−98 1162 CGPG5530.pep Response_reg 504 644 85.4 1.80E−22 1163 CGPG5534.pep Y_phosphatase2 3 169 331.1 2.00E−96 1164 CGPG5537.pep TBP 62 147 136.9 5.90E−38 1164 CGPG5537.pep TBP 152 238 157.1 4.70E−44 1165 CGPG5545.pep CBS 35 175 26.9 7.50E−05 1165 CGPG5545.pep CBS 193 318 80.7 4.60E−21 1166 CGPG555.pep PALP 104 396 325.8 7.90E−95 1166 CGPG555.pep Thr_dehydrat_C 409 498 105.4 1.70E−28 1166 CGPG555.pep Thr_dehydrat_C 504 591 126.4 8.20E−35 1167 CGPG5558.pep Cyclin_N 212 337 208.5 1.60E−59 1167 CGPG5558.pep Cyclin_C 339 458 141 3.30E−39 1168 CGPG5559.pep Suc_Fer-like 69 311 370.5  2.70E−108 1169 CGPG5562.pep Suc_Fer-like 59 308 60.7 4.90E−15 1170 CGPG5592.pep Rho_GDI 35 239 71.2 3.40E−18 1171 CGPG5625.pep LRR_1 433 455 20.5 0.0061  1171 CGPG5625.pep LRR_1 457 476 11.7 2.1   1171 CGPG5625.pep Pkinase 586 854 138.6 1.80E−38 1171 CGPG5625.pep Pkinase_Tyr 587 854 123.3 7.00E−34 1172 CGPG5631.pep WAK 171 270 186.4 7.00E−53 1172 CGPG5631.pep Pkinase_Tyr 390 660 146.8 5.90E−41 1172 CGPG5631.pep Pkinase 390 658 159.5 9.00E−45 1173 CGPG5632.pep Aldedh 29 491 831.6  4.30E−247 1174 CGPG5636.pep Aldedh 15 476 794.5  6.10E−236 1175 CGPG5637.pep Aldedh 32 493 925.9  1.70E−275 1176 CGPG564.pep Aminotran_3 80 413 293.8 3.30E−85 1177 CGPG5641.pep Aldedh 14 472 720.7  1.10E−213 1178 CGPG5650.pep Aminotran_3 32 374 476.5  3.50E−140 1179 CGPG5653.pep Aminotran_1_2 32 383 268.2 1.70E−77 1180 CGPG5657.pep Aldedh 15 474 701.6  5.70E−208 1181 CGPG5671.pep Gp_dh_N 3 151 356.5  4.40E−104 1181 CGPG5671.pep Gp_dh_C 156 313 350.1  3.90E−102 1182 CGPG5672.pep Glutaminase 24 309 615.7  4.20E−182 1183 CGPG5677.pep PGAM 4 165 177.7 3.10E−50 1184 CGPG5678.pep Aminotran_1_2 35 385 204 3.60E−58 1185 CGPG5679.pep TIM 7 248 398.9  8.00E−117 1186 CGPG5682.pep Aminotran_3 31 384 432.3  7.00E−127 1187 CGPG5691.pep PK 5 350 699.4  2.60E−207 1187 CGPG5691.pep PK_C 362 478 198.7 1.40E−56 1188 CGPG5699.pep Gp_dh_N 3 155 274 3.00E−79 1188 CGPG5699.pep Gp_dh_C 160 316 231.1 2.60E−66 1189 CGPG5705.pep NDK 3 137 354.1  2.40E−103 1190 CGPG5722.pep Pyrophosphatase 17 175 197.9 2.50E−56 1191 CGPG5734.pep Cyclin_N 232 357 208.7 1.40E−59 1191 CGPG5734.pep Cyclin_C 359 478 150 6.70E−42 1192 CGPG5736.pep PP2C 22 280 398.6  9.20E−117 1193 CGPG5744.pep CDC50 63 365 697.3  1.20E−206 1194 CGPG5747.pep Pkinase 23 318 294 2.90E−85 1195 CGPG5748.pep NAD_Gly3P_dh_N 84 259 271 2.50E−78 1195 CGPG5748.pep NAD_Gly3P_dh_C 282 432 282.8 6.90E−82 1198 CGPG577.pep Thioredoxin 7 111 138.6 1.70E−38 1199 CGPG5780.pep AA_permease 68 517 −83.3 0.0017  1200 CGPG5793.pep AA_permease 285 815 226.5 5.90E−65 1201 CGPG5795.pep Sugar_tr 123 565 30.1 3.70E−10 1202 CGPG5796.pep Sugar_tr 43 466 340.9 2.30E−99 1202 CGPG5796.pep MFS_1 47 417 74.4 3.70E−19 1203 CGPG5800.pep AA_permease 86 546 489  5.90E−144 1204 CGPG5812.pep Pkinase 22 273 334.2 2.30E−97 1204 CGPG5812.pep Pkinase_Tyr 22 271 85.2 2.10E−22 1205 CGPG5815.pep Pkinase 9 272 136.6 6.90E−38 1206 CGPG5838.pep Pkinase 1 264 137.8 3.10E−38 1207 CGPG5844.pep Pkinase 78 351 159.7 7.80E−45 1207 CGPG5844.pep Pkinase_Tyr 78 351 122.7 1.10E−33 1208 CGPG5846.pep Pkinase_Tyr 92 376 128.5 2.00E−35 1208 CGPG5846.pep Pkinase 99 376 136.1 9.90E−38 1209 CGPG5851.pep Pkinase_Tyr 121 401 138.2 2.30E−38 1209 CGPG5851.pep Pkinase 121 401 139.5 9.70E−39 1210 CGPG5857.pep Pkinase 19 273 159.1 1.20E−44 1211 CGPG5862.pep Pkinase 181 447 99.8 8.50E−27 1211 CGPG5862.pep Pkinase_Tyr 181 447 95.5 1.70E−25 1212 CGPG5863.pep Pkinase 52 330 86.5 8.60E−23 1213 CGPG5867.pep Pkinase_Tyr 142 423 94.1 4.50E−25 1213 CGPG5867.pep Pkinase 142 423 104 4.70E−28 1214 CGPG5872.pep Pkinase_Tyr 18 288 125.8 1.20E−34 1214 CGPG5872.pep Pkinase 18 288 153 7.90E−43 1215 CGPG5913.pep ADH_N 28 109 95.4 1.80E−25 1215 CGPG5913.pep ADH_zinc_N 140 284 151 3.30E−42 1217 CGPG5961.pep Biotin_lipoyl 94 167 79.7 9.50E−21 1217 CGPG5961.pep 2-oxoacid_dh 232 462 478  1.20E−140 1219 CGPG5968.pep Pribosyltran 36 172 151.2 2.90E−42 1220 CGPG5984.pep Pkinase 115 443 246.8 4.70E−71 1221 CGPG5991.pep LRR_1 266 293 9.3 5.7   1222 CGPG6006.pep RRM_1 19 89 81.3 3.10E−21 1223 CGPG6015.pep La 14 85 101.3 3.00E−27 1223 CGPG6015.pep RRM_1 118 188 37.1 6.40E−08 1223 CGPG6015.pep RRM_3 302 404 142.2 1.40E−39 1224 CGPG603.pep G6PD_N 35 222 342 1.00E−99 1224 CGPG603.pep G6PD_C 224 508 655.5  4.50E−194 1225 CGPG6046.pep Str_synth 179 266 137.2 4.80E−38 1226 CGPG6063.pep Nramp 88 451 733.6  1.40E−217 1228 CGPG6092.pep SRPRB 53 235 117.6 3.70E−32 1229 CGPG6104.pep Steroid_dh 111 262 337.7 2.00E−98 1230 CGPG6106.pep LEA_5 1 92 209.3 9.10E−60 1231 CGPG6111.pep PP-binding 48 115 75.2 2.10E−19 1232 CGPG6113.pep UQ_con 7 143 205.4 1.40E−58 1234 CGPG6132.pep SMP 13 71 121.1 3.30E−33 1234 CGPG6132.pep SMP 135 196 113.9 4.90E−31 1234 CGPG6132.pep SMP 200 262 105 2.30E−28 1236 CGPG6147.pep Redoxin 74 234 181.5 2.20E−51 1236 CGPG6147.pep AhpC-TSA 75 214 65.2 2.30E−16 1237 CGPG6152.pep Arf 5 177 434.6  1.40E−127 1237 CGPG6152.pep SRPRB 15 177 −23.5 7.20E−06 1237 CGPG6152.pep Miro 19 129 20.4 0.00012 1237 CGPG6152.pep Ras 19 179 −47.2 8.20E−06 1238 CGPG6154.pep Ion_trans_2 122 204 70 7.90E−18 1238 CGPG6154.pep Ion_trans_2 253 328 48.9 1.80E−11 1239 CGPG6170.pep UQ_con 19 158 187.1 4.50E−53 1240 CGPG6171.pep Thioredoxin 120 227 55.8 1.50E−13 1241 CGPG6177.pep AIG1 39 236 212.9 7.60E−61 1241 CGPG6177.pep MMR_HSR1 39 154 31.5 1.40E−06 1242 CGPG6181.pep Peptidase_C12 2 214 311.3 1.80E−90 1243 CGPG6188.pep Di19 10 217 479  6.00E−141 1244 CGPG6202.pep TB2_DP1_HVA22 9 106 191.2 2.60E−54 1245 CGPG6217.pep MFS_1 40 460 86.7 7.20E−23 1245 CGPG6217.pep Sugar_tr 90 507 −7.3 1.10E−08 1246 CGPG623.pep SATase_N 45 149 210 5.60E−60 1246 CGPG623.pep Hexapep 203 220 19.7 0.011  1246 CGPG623.pep Hexapep 229 246 15.6 0.18   1246 CGPG623.pep Hexapep 247 264 8 16     1247 CGPG6239.pep Sugar_tr 27 458 289.4 7.10E−84 1247 CGPG6239.pep MFS_1 32 413 90.4 5.50E−24 1248 CGPG6244.pep Pkinase 39 303 81.8 2.10E−21 1249 CGPG6254.pep Pkinase 12 264 310.9 2.40E−90 1249 CGPG6254.pep Pkinase_Tyr 12 261 75.1 2.20E−19 1249 CGPG6254.pep NAF 292 352 103 9.50E−28 1251 CGPG627.pep His_biosynth 48 289 33.3 4.00E−12 1252 CGPG6271.pep Pkinase 191 527 227.5 3.00E−65 1253 CGPG6278.pep Pkinase_Tyr 86 365 146.9 5.60E−41 1253 CGPG6278.pep Pkinase 86 368 158.7 1.60E−44 1254 CGPG6288.pep Pkinase 207 463 183.7 4.70E−52 1254 CGPG6288.pep Pkinase_Tyr 207 463 207.1 4.10E−59 1255 CGPG6309.pep PRA1 29 181 233.1 6.50E−67 1256 CGPG633.pep DCP1 12 134 258.3 1.70E−74 1257 CGPG635.pep RmlD_sub_bind 7 338 −145.7 0.00034 1257 CGPG635.pep adh_short 7 177 −35.3 0.0026  1257 CGPG635.pep Epimerase 9 273 226.4 6.40E−65 1257 CGPG635.pep Polysacc_synt_2 9 319 −162.6 0.0011  1257 CGPG635.pep 3Beta_HSD 10 299 −79 3.60E−05 1257 CGPG635.pep NAD_binding_4 11 240 −73 0.00047 1258 CGPG6350.pep LRRNT_2 32 78 22.6 0.0015  1258 CGPG6350.pep LRR_1 105 127 20.8 0.0051  1258 CGPG6350.pep LRR_1 129 151 13.6 0.74   1258 CGPG6350.pep LRR_1 153 175 13.4 0.84   1258 CGPG6350.pep LRR_1 177 196 10.9 2.9   1260 CGPG6365.pep Aminotran_1_2 32 384 403.5  3.20E−118 1261 CGPG6374.pep Gln-synt_C 120 380 370.8  2.30E−108 1262 CGPG6377.pep PGK 2 383 466.4  3.70E−137 1263 CGPG638.pep PA 51 163 106 1.10E−28 1264 CGPG6397.pep NAD_binding_2 1 157 −57 0.00027 1264 CGPG6397.pep NAD_Gly3P_dh_N 2 121 −33.4 0.0009  1264 CGPG6397.pep F420_oxidored 3 246 249.4 7.60E−72 1265 CGPG6398.pep Enolase_N 5 135 212.4 1.10E−60 1265 CGPG6398.pep Enolase_C 140 430 405  1.10E−118 1266 CGPG6408.pep ADH_N 25 155 153.5 6.00E−43 1266 CGPG6408.pep ADH_zinc_N 185 350 101.5 2.50E−27 1267 CGPG6415.pep NTP_transferase 4 271 71.9 2.10E−18 1268 CGPG6421.pep ADH_N 25 148 131.4 2.60E−36 1268 CGPG6421.pep ADH_zinc_N 179 318 163.9 4.30E−46 1269 CGPG6442.pep iPGM_N 2 363 870.1  1.10E−258 1269 CGPG6442.pep Metalloenzyme 373 488 191.4 2.20E−54 1270 CGPG6443.pep PGK 1 391 727.8  7.60E−216 1271 CGPG6446.pep PK 106 453 901.2  4.70E−268 1271 CGPG6446.pep PK_C 467 587 259.4 7.60E−75 1272 CGPG6453.pep Aminotran_1_2 41 402 404.3  1.80E−118 1273 CGPG6466.pep ADH_N 27 153 129.2 1.20E−35 1273 CGPG6466.pep ADH_zinc_N 184 322 135.3 1.80E−37 1274 CGPG6467.pep Aminotran_3 19 366 361.7  1.20E−105 1275 CGPG6470.pep PfkB 1 302 230 5.40E−66 1276 CGPG6475.pep NTP_transferase 10 282 35.5 1.90E−09 1277 CGPG6477.pep NDK 4 138 268.7 1.20E−77 1278 CGPG6478.pep PfkB 1 308 70.6 5.30E−18 1279 CGPG6493.pep AA_permease 94 561 594.7  9.00E−176 1280 CGPG6506.pep Asparaginase 140 457 525.4  6.50E−155 1281 CGPG6518.pep NAD_binding_2 2 173 303 5.60E−88 1281 CGPG6518.pep 6PGD 177 467 700.7  1.10E−207 1282 CGPG6546 pep PK 3 348 560.5  1.80E−165 1282 CGPG6546.pep PK_C 360 477 86.8 6.80E−23 1283 CGPG6556.pep Aminotran_1_2 124 475 223.7 4.30E−64 1284 CGPG6562.pep Aminotran_3 116 451 628.8  4.90E−186 1285 CGPG6566.pep NTP_transferase 95 350 301.4 1.80E−87 1285 CGPG6566.pep Hexapep 398 415 6.4 25     1285 CGPG6566.pep Hexapep 432 449 16.6 0.097  1285 CGPG6566.pep Hexapep 460 477 5.5 31     1286 CGPG6571.pep Aldedh 102 560 720.7  1.10E−213 1287 CGPG6576.pep Aldedh 99 565 569.2  4.30E−168 1288 CGPG659.pep G_glu_transpept 48 567 839.1  2.30E−249 1289 CGPG6594.pep DAO 94 524 −28.6 0.00082 1289 CGPG6594.pep GIDA 94 429 −226.6 0.0045  1289 CGPG6594.pep Pyr_redox_2 94 419 229.8 6.20E−66 1289 CGPG6594.pep Pyr_redox 278 374 119.5 9.90E−33 1289 CGPG6594.pep Pyr_redox_dim 450 559 194.7 2.20E−55 1290 CGPG6603.pep Pyr_redox_2 94 397 239.1 9.60E−69 1290 CGPG6603.pep Pyr_redox 257 350 101.2 3.10E−27 1290 CGPG6603.pep Pyr_redox_dim 427 538 189.7 7.10E−54 1291 CGPG6608.pep DAO 93 497 −33.9 0.0018  1291 CGPG6608.pep Pyr_redox_2 93 394 145.4 1.60E−40 1291 CGPG6608.pep Pyr_redox 256 348 92.2 1.70E−24 1291 CGPG6608.pep Pyr_redox_dim 423 532 89.3 1.20E−23 1292 CGPG6634.pep DUF177 100 252 152.3 1.30E−42 1294 CGPG6667.pep Invertase_neut 89 577 1313.4 0     1295 CGPG6678.pep Biotin_lipoyl 92 165 75.9 1.30E−19 1295 CGPG6678.pep E3_binding 225 263 51.7 2.60E−12 1295 CGPG6678.pep 2-oxoacid_dh 281 512 374.6  1.60E−109 1296 CGPG6695.pep GIDA 97 428 −211.9 0.00053 1296 CGPG6695.pep Pyr_redox_2 97 408 266.1 7.40E−77 1296 CGPG6695.pep Pyr_redox 266 361 90.1 7.20E−24 1296 CGPG6695.pep Pyr_redox_dim 436 545 184.3 3.20E−52 1297 CGPG6699.pep Ribul_P_3_epim 94 295 491.3  1.20E−144 1298 CGPG670.pep Fer2 60 135 120.2 6.20E−33 1299 CGPG6705.pep PK 89 433 788.8  3.30E−234 1299 CGPG6705.pep PK_C 445 559 164.3 3.30E−46 1299 CGPG6705.pep PEP-utilizers 584 663 122.9 9.40E−34 1300 CGPG6735.pep FBPase 93 413 525  8.60E−155 1301 CGPG6744.pep Glycolytic 92 429 576.6  2.40E−170 1302 CGPG6753.pep Pyr_redox 236 328 10.7 0.00051 1302 CGPG6753.pep Pyr_redox_2 236 538 72.9 1.10E−18 1303 CGPG6757.pep Aminotran_1_2 127 473 234 3.30E−67 1305 CGPG6806.pep mTERF 110 457 550.4  2.00E−162 1306 CGPG6811.pep GH3 10 567 1341 0     1308 CGPG6815.pep V-ATPase_G 5 109 183.9 4.00E−52 1310 CGPG6830.pep Tbf5 13 76 113.7 5.40E−31 1313 CGPG6864.pep DUF620 190 438 698.7  4.50E−207 1314 CGPG6877.pep Hep_59 101 194 198.3 1.90E−56 1315 CGPG6878.pep Peptidase_M24 107 343 229.5 7.80E−66 1316 CGPG6880.pep PAP_fibrillin 72 232 178.2 2.20E−50 1318 CGPG6887.pep AIG2 12 111 89.1 1.40E−23 1319 CGPG6895.pep zf-CCHC 166 183 26 0.00014 1319 CGPG6895.pep zf-CCHC 208 225 24.9 0.00026 1319 CGPG6895.pep zf-CCHC 325 342 38.1 3.30E−08 1319 CGPG6895.pep zf-CCHC 356 373 32 2.20E−06 1322 CGPG6912.pep zf-DHHC 149 213 119.1 1.30E−32 1324 CGPG6942.pep RNA_pol_Rpb5_N 18 108 174.3 3.20E−49 1324 CGPG6942.pep RNA_pol_Rpb5_C 149 222 68.2 2.80E−17 1327 CGPG6969.pep 2OG-FeII_Oxy 223 323 152.3 1.30E−42 1329 CGPG6991.pep Glyco_tran_28_C 11 170 171.7 1.90E−48 1332 CGPG7037.pep Sad1_UNC 313 416 −3.4 0.0011  1333 CGPG7051.pep PAP_fibrillin 84 236 218.7 1.40E−62 1336 CGPG7086.pep SFT2 44 163 182.6 9.70E−52 1339 CGPG7136.pep NOI 1 72 159.7 8.10E−45 1340 CGPG7147.pep RAMP4 1 64 152.5 1.20E−42 1343 CGPG7222.pep Branch 49 274 399.8  4.00E−117 1345 CGPG7233.pep eIF2A 214 407 415.3  8.90E−122 1346 CGPG7238.pep UPF0185 5 80 214.1 3.30E−61 1347 CGPG7253.pep ArfGap 15 117 58.4 2.40E−14 1348 CGPG7255.pep Arf 5 177 365.3  1.00E−106 1348 CGPG7255.pep SRPRB 15 200 −3.7 2.60E−07 1348 CGPG7255.pep Miro 19 129 40.3 7.10E−09 1348 CGPG7255.pep Ras 19 179 −43.7 4.50E−06 1349 CGPG7286.pep ORC2 20 345 558.7  6.00E−165 1350 CGPG7292.pep Methyltransf_11 38 135 44.1 5.00E−10 1350 CGPG7292.pep Methyltransf_12 38 133 38.4 2.60E−08 1351 CGPG7301.pep ELFV_dehydrog_N 57 187 294.9 1.50E−85 1351 CGPG7301.pep ELFV_dehydrog 202 445 484.3  1.50E−142 1352 CGPG7305.pep DAO 126 401 −31.6 0.0013  1352 CGPG7305.pep Pyr_redox_2 126 386 66.3 1.00E−16 1352 CGPG7305.pep Pyr_redox 255 345 55.7 1.60E−13 1353 CGPG7307.pep Gp_dh_N 11 163 300.6 3.00E−87 1353 CGPG7307.pep Gp_dh_C 168 324 258.5 1.50E−74 1354 CGPG7318.pep MIP 1 142 −31.2 9.10E−08 1355 CGPG7319.pep SNF5 172 400 471.8  9.00E−139 1356 CGPG7345.pep Lipase_3 97 237 131.1 3.30E−36 1357 CGPG7368.pep MT-A70 516 676 316.4 5.20E−92 1358 CGPG7385.pep FHA 32 107 51 4.10E−12 1359 CGPG7391.pep G-patch 6 50 71.2 3.40E−18 1360 CGPG7405.pep TATA_RF 1 216 160.8 3.70E−45 1361 CGPG7415.pep IU_nuc_hydro 1 312 255.3 1.30E−73 1362 CGPG7416.pep GLTP 52 233 208 2.30E−59 1363 CGPG7420.pep PRK 95 302 426.6  3.60E−125 1366 CGPG7445.pep PRC 92 169 37.2 5.70E−08 1366 CGPG7445.pep PRC 171 252 48.6 2.20E−11 1367 CGPG7465.pep Aldedh 103 567 834.4  6.30E−248 1368 CGPG7473.pep F-box 273 320 35.1 2.60E−07 1368 CGPG7473.pep WD40 412 449 41.5 2.90E−09 1368 CGPG7473.pep WD40 453 493 49.7 1.00E−11 1368 CGPG7473.pep WD40 520 556 30.6 5.70E−06 1368 CGPG7473.pep WD40 560 598 41.7 2.70E−09 1369 CGPG7489.pep UBX 295 376 70.8 4.50E−18 1370 CGPG7492.pep Pescadillo_N 8 291 519  5.30E−153 1370 CGPG7492.pep BRCT 337 414 50.7 5.00E−12 1371 CGPG7499.pep G-alpha 423 839 50.2 3.20E−22 1374 CGPG7508.pep Smg4_UPF3 1 170 236.2 7.10E−68 1375 CGPG7509.pep SSB 76 187 95.3 1.90E−25 1376 CGPG7511.pep GFA 31 125 74.2 4.20E−19 1377 CGPG7515.pep Brix 45 297 232.5 9.60E−67 1378 CGPG7521.pep G-alpha 23 386 560.5  1.80E−165 1380 CGPG7547.pep PAD_porph 14 368 695.7  3.40E−206 1381 CGPG7561.pep Snf7 17 187 219.6 7.40E−63 1382 CGPG7562.pep Sybindin 6 136 253.6 4.30E−73 1382 CGPG7562.pep Sedlin_N 11 135 −21.6 0.00015 1383 CGPG7563.pep DUF887 40 279 394.2  2.10E−115 1384 CGPG7567.pep Peptidase_M18 14 461 680  1.90E−201 1389 CGPG7597.pep zf-AN1 76 116 78.4 2.40E−20 1390 CGPG7606.pep Pentapeptide 127 166 29.2 1.50E−05 1390 CGPG7606.pep Pentapeptide 172 211 42.7 1.30E−09 1392 CGPG7637.pep DAD 2 112 168.4 1.90E−47 1393 CGPG7649.pep YgbB 71 227 244.8 2.00E−70 1394 CGPG7658.pep Cyclase 56 256 109.9 7.70E−30 1395 CGPG7664.pep Aldedh 9 463 801  7.20E−238 1396 CGPG7666.pep Aminotran_1_2 26 392 491  1.50E−144 1397 CGPG7668.pep DUF594 660 719 97.6 3.90E−26 1399 CGPG7746.pep UPF0153 49 139 59.7 9.90E−15 1400 CGPG7747.pep Copine 113 261 308.5 1.30E−89 1401 CGPG7752.pep zf-MYND 176 214 48.9 1.80E−11 1401 CGPG7752.pep PDCD2_C 241 403 38.2 1.00E−10 1403 CGPG7770.pep YTH 263 353 218.6 1.40E−62 1406 CGPG7778.pep Ubie_methyltran 51 304 393.3  3.70E−115 1406 CGPG7778.pep Methyltransf_11 105 222 75 2.50E−19 1406 CGPG7778.pep Methyltransf_12 105 220 43.1 1.00E−09 1407 CGPG7786.pep KH_1 141 193 27.6 4.60E−05 1408 CGPG7788.pep YIF1 34 263 341.8 1.20E−99 1410 CGPG78.pep Hpt 46 132 55.5 1.80E−13 1411 CGPG783.pep RRM_1 288 354 40 8.40E−09 1411 CGPG783.pep RRM_2 682 778 232.4 1.00E−66 1412 CGPG7832.pep STT3 26 670 626.4  2.50E−185 1413 CGPG7841.pep ECH 17 186 192.8 8.40E−55 1413 CGPG7841.pep 3HCDH_N 311 490 295.4 1.10E−85 1413 CGPG7841.pep 3HCDH 492 585 116.2 9.50E−32 1414 CGPG7845.pep LRRNT_2 23 64 49.2 1.50E−11 1414 CGPG7845.pep LRR_1 97 119 10.5 3.5   1414 CGPG7845.pep LRR_1 121 143 14.5 0.39   1414 CGPG7845.pep LRR_1 145 167 12.1 1.7   1414 CGPG7845.pep LRR_1 169 192 13.1 1.1   1414 CGPG7845.pep LRR_1 194 216 14 0.55   1415 CGPG7847.pep Peptidase_C48 30 225 −1.9 0.00023 1417 CGPG7853.pep LRR_1 142 164 17.4 0.052  1417 CGPG7853.pep LRR_1 166 188 9.9 4.4   1417 CGPG7853.pep LRR_1 190 212 10 4.3   1417 CGPG7853.pep LRR_1 214 235 13.8 0.65   1417 CGPG7853.pep LRR_1 258 280 10.5 3.5   1417 CGPG7853.pep LRR_1 282 304 14 0.56   1417 CGPG7853.pep LRR_1 306 325 11.7 2.1   1418 CGPG7857.pep Response_reg 79 195 89.7 9.40E−24 1418 CGPG7857.pep CCT 689 736 62.1 1.80E−15 1420 CGPG7869.pep Acyltransferase 117 264 81.9 2.00E−21 1421 CGPG7891.pep FMO-like 11 427 −207 1.20E−16 1421 CGPG7891.pep DAO 13 268 −9.4 4.70E−05 1422 CGPG7892.pep FMO-like 9 416 −157.4 2.80E−19 1423 CGPG7906.pep Skp1_POZ 4 65 96.7 7.50E−26 1423 CGPG7906.pep Skp1 76 153 154.3 3.40E−43 1424 CGPG7924.pep AAA 249 462 54.2 4.60E−13 1428 CGPG7964.pep IQ 108 128 25.7 0.00017 1428 CGPG7964.pep IQ 130 150 12.2 1.9   1429 CGPG7968.pep FMO-like 13 427 −229.9 2.10E−15 1429 CGPG7968.pep DAO 15 291 −34.2 0.0019  1429 CGPG7968.pep Pyr_redox_2 15 321 −18 0.00054 1431 CGPG7972.pep FAD_binding_3 5 372 −97.4 5.20E−06 1432 CGPG7982.pep Tetraspannin 4 241 241.9 1.40E−69 1433 CGPG7985.pep BT1 57 469 419.2  6.00E−123 1434 CGPG7993.pep F-box 27 73 15.1 0.26   1434 CGPG7993.pep LRR_2 278 304 16.8 0.084  1435 CGPG8.pep p450 39 503 399  7.30E−117 1436 CGPG80.pep Pkinase 68 328 277.6 2.60E−80 1437 CGPG8001.pep FMO-like 13 433 −243.5 1.10E−14 1437 CGPG8001.pep Pyr_redox 215 295 5.3 0.0016  1438 CGPG8009.pep BT1 41 511 517.8  1.30E−152 1440 CGPG8049.pep BT1 1 436 331.8 1.20E−96 1441 CGPG806.pep Synaptobrevin 127 215 146.7 6.20E−41 1442 CGPG8060.pep DUF829 161 425 426  5.30E−125 1446 CGPG81.pep Pkinase 70 330 287.7 2.30E−83 1452 CGPG8125.pep zf-C3HC4 46 86 31.1 4.00E−06 1453 CGPG8134.pep DEK_C 3 57 60.4 6.10E−15 1453 CGPG8134.pep SWIB 197 272 140.9 3.60E−39 1453 CGPG8134.pep SWIB 305 382 112.9 9.40E−31 1455 CGPG8156.pep PCI 258 362 69.4 1.20E−17 1456 CGPG8159.pep ACT 77 141 51.9 2.10E−12 1456 CGPG8159.pep ACT 308 374 51.5 3.00E−12 1458 CGPG8179.pep WD40 138 177 23.7 0.00069 1458 CGPG8179.pep WD40 264 305 42.5 1.50E−09 1459 CGPG8193.pep Ank 22 54 5.5 5.2   1459 CGPG8193.pep Ank 55 87 36.4 1.00E−07 1460 CGPG8197.pep F-box 5 53 22 0.0022  1461 CGPG8198.pep F-box 74 119 15 0.28   1461 CGPG8198.pep Kelch_2 174 221 19.7 0.011  1461 CGPG8198.pep Kelch_1 223 278 15.6 0.041  1461 CGPG8198.pep Kelch_2 329 369 14.2 0.51   1463 CGPG8211.pep F-box 182 229 48.8 2.00E−11 1463 CGPG8211.pep WD40 292 328 30.3 6.90E−06 1463 CGPG8211.pep WD40 332 368 37.7 4.30E−08 1463 CGPG8211.pep WD40 372 408 43.4 8.30E−10 1463 CGPG8211.pep WD40 411 449 40.9 4.60E−09 1463 CGPG8211.pep WD40 453 538 32.2 1.90E−06 1463 CGPG8211.pep WD40 542 578 38.9 1.80E−08 1464 CGPG823.pep Ribosomal_S6e 1 129 258.3 1.70E−74 1466 CGPG8238.pep PGI 49 537 857.4  7.40E−255 1467 CGPG8260.pep Iso_dh 4 331 460.7  1.90E−135 1468 CGPG8267.pep Pyridoxal_deC 34 383 352.2  8.70E−103 1469 CGPG8268.pep NIR_SIR_ferr 62 131 43.9 5.60E−10 1469 CGPG8268.pep NIR_SIR 164 345 193.4 5.50E−55 1469 CGPG8268.pep NIR_SIR_ferr 360 432 76.9 6.80E−20 1470 CGPG8274.pep PK 5 347 589.9  2.50E−174 1470 CGPG8274.pep PK_C 363 476 81.9 2.10E−21 1471 CGPG8277.pep Rib_5-P_isom_A 55 229 345  1.30E−100 1472 CGPG8279.pep F-box 22 69 43 1.10E−09 1472 CGPG8279.pep Kelch_1 124 168 35.2 2.40E−07 1472 CGPG8279.pep Kelch_1 170 213 29.4 1.40E−05 1472 CGPG8279.pep Kelch_2 170 213 24.3 0.00045 1475 CGPG8408.pep DUF641 60 192 237.3 3.40E−68 1476 CGPG842.pep Redoxin 5 162 182.6 9.80E−52 1476 CGPG842.pep AhpC-TSA 6 142 38.6 2.20E−08 1477 CGPG8421.pep NOSIC 121 173 90.1 6.90E−24 1477 CGPG8421.pep Nop 213 361 257.3 3.20E−74 1478 CGPG8435.pep NHL 55 82 5.9 3.4   1478 CGPG8435.pep NHL 115 142 37.2 5.80E−08 1479 CGPG8440.pep U-box 242 316 70.2 6.80E−18 1479 CGPG8440.pep Arm 372 413 47.5 4.70E−11 1479 CGPG8440.pep Arm 455 495 32.1 2.00E−06 1479 CGPG8440.pep Arm 496 537 22.3 0.0018  1479 CGPG8440.pep Arm 538 578 25.5 0.0002  1480 CGPG8453.pep ACT 36 99 33.5 7.90E−07 1480 CGPG8453.pep ACT 129 201 54.1 4.90E−13 1480 CGPG8453.pep ACT 265 332 28.6 2.40E−05 1480 CGPG8453.pep ACT 343 406 43.5 7.50E−10 1481 CGPG8470.pep DUF89 18 357 −103.6 0.0022  1482 CGPG8479.pep F-box 31 78 22.6 0.0015  1482 CGPG8479.pep Kelch_1 124 170 35.4 2.00E−07 1482 CGPG8479.pep Kelch_1 172 216 44.6 3.40E−10 1482 CGPG8479.pep Kelch_2 172 216 21.7 0.0027  1483 CGPG8489.pep F-box 3 50 44.4 3.90E−10 1483 CGPG8489.pep FBA_1 219 384 291.3 2.00E−84 1484 CGPG8498.pep Fcf1 87 185 245.9 9.10E−71 1485 CGPG85.pep Aa_trans 19 454 556.5  2.80E−164 1486 CGPG8501.pep PPR 149 183 11.6 0.32   1486 CGPG8501.pep PPR 189 223 29 1.70E−05 1486 CGPG8501.pep PPR 224 258 25.6 0.00019 1486 CGPG8501.pep PPR 259 292 6.5 1.3   1486 CGPG8501.pep PPR 330 364 4.2 2.5   1486 CGPG8501.pep PPR 401 435 12.3 0.27   1487 CGPG8507.pep DUF588 31 185 202.1 1.30E−57 1488 CGPG8509.pep Pro_isomerase 80 233 18.3 3.90E−10 1490 CGPG8517.pep B_lectin 84 197 191 2.90E−54 1490 CGPG8517.pep S_locus_glycop 211 339 250 5.20E−72 1490 CGPG8517.pep PAN_2 356 422 105.1 2.10E−28 1492 CGPG852.pep Ribosomal_S5 94 160 140.9 3.60E−39 1492 CGPG852.pep Ribosomal_S5_C 177 250 134.4 3.30E−37 1498 CGPG8567.pep TB2_DP1_HVA22 3 98 59.4 1.20E−14 1499 CGPG8580.pep Caleosin 22 195 434.3  1.70E−127 1501 CGPG8590.pep DUF579 42 289 571.9  6.60E−169 1503 CGPG8594.pep DUF584 1 139 248.7 1.30E−71 1504 CGPG8606.pep Exo_endo_phos 56 327 125 2.30E−34 1505 CGPG8628.pep DUF584 32 203 125.8 1.30E−34 1507 CGPG8654.pep PPR 73 107 13.2 0.21   1507 CGPG8654.pep PPR 141 175 38.6 2.30E−08 1508 CGPG8668.pep TATA_RF 1 200 306.9 3.90E−89 1511 CGPG8702.pep RPE65 50 622 19.9 1.70E−17 1514 CGPG8748.pep AAA 201 357 13.1 1.30E−06 1516 CGPG8770.pep DUF543 1 73 107.6 3.90E−29 1517 CGPG8777.pep DUF569 1 144 377.9  1.70E−110 1517 CGPG8777.pep DUF569 227 368 391.4  1.40E−114 1519 CGPG8786.pep DUF260 13 113 247.6 2.70E−71 1520 CGPG8792.pep Abhydrolase_3 75 290 228.4 1.60E−65 1521 CGPG8801.pep PPR 110 144 18.7 0.022  1521 CGPG8801.pep PPR 145 179 9.1 0.64   1521 CGPG8801.pep PPR 181 215 42.6 1.40E−09 1521 CGPG8801.pep PPR 216 250 19.5 0.012  1521 CGPG8801.pep PPR 251 285 23.6 0.00076 1521 CGPG8801.pep PPR 286 320 37.2 6.10E−08 1521 CGPG8801.pep PPR 321 355 12 0.3   1522 CGPG8809.pep Ribosomal_L12 141 208 61.2 3.50E−15 1523 CGPG8840.pep CLP_protease 115 289 45.1 1.30E−11 1524 CGPG8850.pep PPR 189 223 17.3 0.057  1524 CGPG8850.pep PPR 224 258 48.5 2.40E−11 1524 CGPG8850.pep PPR 297 331 34.6 3.50E−07 1524 CGPG8850.pep PPR 332 366 46.2 1.20E−10 1524 CGPG8850.pep PPR 367 401 40.7 5.40E−09 1524 CGPG8850.pep PPR 402 436 50 8.00E−12 1524 CGPG8850.pep PPR 437 470 36.5 9.50E−08 1524 CGPG8850.pep PPR 471 505 39.8 9.60E−09 1524 CGPG8850.pep PPR 506 540 23.2 0.00094 1524 CGPG8850.pep PPR 542 576 46.6 8.80E−11 1525 CGPG8870.pep Fructosamin_kin 54 339 208 2.30E−59 1525 CGPG8870.pep APH 69 308 80.1 7.30E−21 1526 CGPG8871.pep DUF59 36 115 57.6 4.20E−14 1527 CGPG8872.pep RRM_1 138 205 78 3.00E−20 1527 CGPG8872.pep RRM_1 214 288 32.4 1.70E−06 1527 CGPG8872.pep RRM_1 308 378 60 8.10E−15 1528 CGPG8876.pep SFT2 43 162 194.7 2.40E−55 1529 CGPG8902.pep RNA_pol_I_A49 31 415 702.7  2.70E−208 1530 CGPG8904.pep G-alpha 103 447 513.2  3.10E−151 1531 CGPG8907.pep DnaJ 4 67 128.7 1.70E−35 1531 CGPG8907.pep zf-C2H2 338 362 28 3.40E−05 1532 CGPG8914.pep Whi5 181 205 50.1 7.80E−12 1533 CGPG8931.pep eIF3_subunit 1 231 272.1 1.20E−78 1534 CGPG8933.pep MACPF 126 322 60.6 5.20E−15 1535 CGPG8935.pep Pkinase 33 324 308.5 1.30E−89 1536 CGPG8938.pep Pkinase 71 348 187.5 3.40E−53 1536 CGPG8938.pep Pkinase_Tyr 71 348 128.4 2.10E−35 1537 CGPG8944.pep PH 31 134 48.5 2.40E−11 1538 CGPG895.pep DUF231 251 427 223.7 4.30E−64 1540 CGPG8961.pep Dus 59 392 236.5 5.90E−68 1541 CGPG8963.pep Pkinase 319 612 332 1.10E−96 1542 CGPG898.pep DUF231 276 448 289.8 5.30E−84 1543 CGPG8993.pep AAA 44 226 54.9 2.80E−13 1543 CGPG8993.pep Rep_fac_C 237 326 113.5 6.50E−31 1544 CGPG8994.pep Brix 86 262 264.3 2.50E−76 1545 CGPG8995.pep Porin_3 54 326 280.1 4.30E−81 1546 CGPG90.pep MFS_1 68 427 55 2.50E−13 1547 CGPG900.pep DUF231 241 420 229.6 6.90E−66 1548 CGPG9002.pep CTP_transf_1 51 382 443.1  3.90E−130 1549 CGPG9009.pep Alg6_Alg8 22 514 439.6  4.30E−129 1550 CGPG9011.pep OTCace_N 70 212 188.6 1.60E−53 1550 CGPG9011.pep OTCace 216 369 198.1 2.20E−56 1551 CGPG9012.pep FolB 16 129 125 2.10E−34 1552 CGPG9017.pep DMRL_synthase 70 213 195.5 1.30E−55 1553 CGPG9025.pep Glyco_transf_29 105 355 −11 1.90E−06 1554 CGPG9026.pep Adap_comp_sub 160 428 469.4  4.70E−138 1555 CGPG9032.pep RNase_PH 33 165 135.6 1.40E−37 1555 CGPG9032.pep RNase_PH_C 194 262 44.9 2.70E−10 1556 CGPG9040.pep Sec1 35 592 217.7 2.70E−62 1557 CGPG9044.pep Syntaxin 57 163 93.9 5.10E−25 1557 CGPG9044.pep SNARE 256 318 79.5 1.10E−20 1558 CGPG9048.pep RNase_PH 15 135 53.3 8.30E−13 1559 CGPG9049.pep Glycos_transf_1 244 442 16 3.70E−05 1560 CGPG9058.pep RNA_pol_N 1 60 125.6 1.40E−34 1561 CGPG906.pep PPR 210 244 28.2 3.10E−05 1561 CGPG906.pep PPR 245 279 13.7 0.19   1562 CGPG9070.pep ATP-synt_C 20 85 42.4 1.60E−09 1562 CGPG9070.pep ATP-synt_C 104 169 21.7 0.00014 1564 CGPG9084.pep CH 15 116 47.4 5.20E−11 1564 CGPG9084.pep EB1 209 255 79.7 9.20E−21 1566 CGPG9098.pep DUF6 32 165 22.6 0.0015  1566 CGPG9098.pep TPT 199 337 −10.3 0.0023  1566 CGPG9098.pep DUF6 208 337 66.1 1.20E−16 1567 CGPG9099.pep Rick_17 kDa_Anti 66 110 24.9 0.00029 1568 CGPG9110.pep RALF 53 118 122.9 9.30E−34 1569 CGPG9119.pep PTR2 115 504 350.4  3.10E−102 1570 CGPG9125.pep ThiF 98 233 171.7 1.90E−48 1571 CGPG913.pep PPR 86 120 32.9 1.20E−06 1571 CGPG913.pep PPR 188 222 51.1 4.00E−12 1571 CGPG913.pep PPR 223 257 7.4 1     1571 CGPG913.pep PPR 289 323 26 0.00014 1571 CGPG913.pep PPR 325 358 12 0.29   1571 CGPG913.pep PPR 361 395 12.8 0.24   1574 CGPG9164.pep DHBP_synthase 5 202 475.9  5.10E−140 1574 CGPG9164.pep GTP_cyclohydro2 207 377 431.4  1.30E−126 1575 CGPG9172.pep Sec61_beta 32 77 83 9.60E−22 1577 CGPG9185.pep DUF423 10 115 84.7 2.90E−22 1578 CGPG9187.pep Pkinase 12 263 298.2 1.60E−86 1579 CGPG9190.pep DREPP 2 203 280.3 3.80E−81 1580 CGPG9193.pep GATase 11 196 175.1 1.90E−49 1580 CGPG9193.pep GMP_synt_C 432 524 172.7 9.30E−49 1581 CGPG9195.pep DUF1279 91 193 127 5.60E−35 1582 CGPG9203.pep Na_H_Exchanger 13 391 242.3 1.00E−69 1582 CGPG9203.pep TrkA_C 418 486 58.4 2.50E−14 1583 CGPG9209.pep GATase 9 197 199.6 7.80E−57 1583 CGPG9209.pep GMP_synt_C 423 515 201.4 2.20E−57 1585 CGPG9210.pep Na_H_Exchanger 10 376 229 1.10E−65 1585 CGPG9210.pep TrkA_N 402 517 131 3.50E−36 1586 CGPG9211.pep NTP_transferase 7 296 508.1  1.00E−149 1586 CGPG9211.pep MannoseP_isomer 307 473 454  2.00E−133 1586 CGPG9211.pep Cupin_2 388 458 48.1 3.10E−11 1587 CGPG9212.pep ATP-synt_ab_N 22 87 53.4 7.60E−13 1587 CGPG9212.pep ATP-synt_ab 143 353 429.3  5.40E−126 1588 CGPG9216.pep DHBP_synthase 10 206 377.8  1.70E−110 1588 CGPG9216.pep GTP_cyclohydro2 211 379 395.3  9.20E−116 1589 CGPG9226.pep Carboxyl_trans 40 541 967.5  5.20E−288 1590 CGPG9252.pep CDC48_N 28 114 132.1 1.60E−36 1590 CGPG9252.pep AAA 245 429 330.3 3.40E−96 1590 CGPG9252.pep AAA_5 245 377 9.8 0.00052 1590 CGPG9252.pep AAA 518 705 344.1  2.40E−100 1592 CGPG9289.pep LSM 10 75 64.8 3.00E−16 1593 CGPG9298.pep p450 41 516 138.8 1.60E−38 1594 CGPG9299.pep ThiF 82 227 145.2 1.80E−40 1597 CGPG9316.pep ATP-grasp_2 34 242 405.7  7.10E−119 1597 CGPG9316.pep Ligase_CoA 285 421 229 1.10E−65 1598 CGPG9317.pep DUF163 43 196 205.3 1.50E−58 1599 CGPG9318.pep Aldo_ket_red 20 285 408  1.40E−119 1600 CGPG9324.pep Pkinase 158 706 150.9 3.40E−42 1601 CGPG9357.pep Raffinose_syn 7 757 1669.7 0     1602 CGPG965.pep Hexapep 70 87 10.5 6.4   1602 CGPG965.pep Hexapep 119 136 16.4 0.11   1602 CGPG965.pep Hexapep 142 159 5.9 28     1602 CGPG965.pep Hexapep 160 177 2.6 71     1603 CGPG970.pep NPH3 206 441 272 1.20E−78 1604 CGPG982.pep p450 29 495 389.8  4.30E−114 1605 CGPG994.pep adh_short 50 218 46.7 8.30E−11 1606 CGPG996.pep DUF866 1 167 456.5  3.60E−134

TABLE 22 Pfam domain gathering name Accession # cutoff domain description 2OG-Fell_Oxy PF03171.11 11.5 2OG-Fe(II) oxygenase superfamily 3Beta_HSD PF01073.10 −135.9 3-beta hydroxysteroid dehydrogenase/isomerase family 3HCDH PF00725.13 −8.9 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain 3HCDH_N PF02737.9  −82.1 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 6PGD PF00393.10 −232.3 6-phosphogluconate dehydrogenase, C-terminal domain AAA PF00004.20 12.3 ATPase family associated with various cellular activities (AAA) AAA_5 PF07728.5  4 ATPase family associated with various cellular activities (AAA) AARP2CN PF08142.3  25 AARP2CN (NUC121) domain AA_kinase PF00696.19 −40 Amino acid kinase family AA_permease PF00324.12 −120.8 Amino acid permease ABC_tran PF00005.18 9.5 ABC transporter ACBP PF00887.10 −14 Acyl CoA binding protein ACP_syn_III_C PF08541.1  −21.6 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ACT PF01842.16 0.7 ACT domain ADH_N PF08240.3  −14.5 Alcohol dehydrogenase GroES-like domain ADH_zinc_N PF00107.17 23.8 Zinc-binding dehydrogenase AIG1 PF04548.7  −40 AIG1 family AIG2 PF06094.3  12.7 AIG2-like family AP2 PF00847.11 21.7 AP2 domain APH PF01636.14 32.5 Phosphotransferase enzyme family ATP-grasp_2 PF08442.1  −118.8 ATP-grasp domain ATP-synt_C PF00137.12 5 ATP synthase subunit C ATP-synt_G PF04718.6  −7.9 Mitochondrial ATP synthase g subunit ATP-synt_ab PF00006.16 −37.5 ATP synthase alpha/beta family, nucleotide-binding domain ATP-synt_ab_N PF02874.14 17 ATP synthase alpha/beta family, beta-barrel domain ATP_bind_1 PF03029.8  −19 Conserved hypothetical ATP binding protein AWPM-19 PF05512.2  25 AWPM-19-like family Aa_trans PF01490.9  −128.4 Transmembrane amino acid transporter protein Abhydrolase_3 PF07859.4  25.8 alpha/beta hydrolase fold Acetyltransf_1 PF00583.15 18.6 Acetyltransferase (GNAT) family Acyltransferase PF01553.12 2.2 Acyltransferase Adap_comp_sub PF00928.12 −5.4 Adaptor complexes medium subunit family AhpC-TSA PF00578.12 4.8 AhpC/TSA family Alba PF01918.12 20 Alba Aldedh PF00171.13 −208.2 Aldehyde dehydrogenase family Aldo_ket_red PF00248.12 −97 Aldo/keto reductase family Alg6_Alg8 PF03155.6  −235.5 ALG6, ALG8 glycosyltransferase family Alpha-amyl_C2 PF07821.3  25 Alpha-amylase C-terminal beta-sheet domain Alpha-amylase PF00128.15 −92.6 Alpha amylase, catalytic domain Aminotran_1_2 PF00155.12 −57.5 Aminotransferase class I and II Aminotran_3 PF00202.12 −206.1 Aminotransferase class-III Aminotran_5 PF00266.10 −164.4 Aminotransferase class-V Ank PF00023.21 0 Ankyrin repeat Arf PF00025.12 40 ADP-ribosylation factor family ArfGap PF01412.9  −17 Putative GTPase activating protein for Arf Arm PF00514.14 17 Armadillo/beta-catenin-like repeat Asp PF00026.14 −153.8 Eukaryotic aspartyl protease Asparaginase PF00710.11 25 Asparaginase Auxin_inducible PF02519.5  −15 Auxin responsive protein B3 PF02362.12 26.5 B3 DNA binding domain BRCT PF00533.17 27.8 BRCA1 C Terminus (BRCT) domain BT1 PF03092.7  −148.6 BT1 family B_lectin PF01453.15 28.2 D-mannose binding lectin Band_7 PF01145.16 10.3 SPFH domain/Band 7 family Beta_elim_lyase PF01212.12 −110.3 Beta-eliminating lyase Biotin_lipoyl PF00364.13 −2.3 Biotin-requiring enzyme Bombesin PF02044.8  11.4 Bombesin-like peptide Branch PF02485.12 −83.5 Core-2/I-Branching enzyme Brix PF04427.9  11.4 Brix domain Bromodomain PF00439.16 8.9 Bromodomain C1_1 PF00130.13 11.4 Phorbol esters/diacylglycerol binding domain (C1 domain) C1_2 PF03107.7  26.4 C1 domain C1_3 PF07649.3  25 C1-like domain C2 PF00168.21 3.7 C2 domain CAF1 PF04857.11 −100.5 CAF1 family ribonuclease CBFD_NFYB_HMF PF00808.14 18.4 Histone-like transcription factor (CBF/NF-Y) and archaeal histone CBS PF00571.19 17.5 CBS domain pair CCT PF06203.5  25 CCT motif CDC48_N PF02359.9  −2 Cell division protein 48 (CDC48), N-terminal domain CDC50 PF03381.6  25 LEM3 (ligand-effect modulator 3) family/CDC50 family CDP-OH_P_transf PF01066.12 0 CDP-alcohol phosphatidyltransferase CH PF00307.22 22.5 Calponin homology (CH) domain CLP_protease PF00574.14 −77.2 Clp protease CPSase_sm_chain PF00988.13 25 Carbamoyl-phosphate synthase small chain, CPSase domain CRAL_TRIO PF00650.11 −26 CRAL/TRIO domain CRAL_TRIO_N PF03765.6  16 CRAL/TRIO, N-terminus CTP_transf_1 PF01148.11 −35.9 Cytidylyltransferase family Caleosin PF05042.4  25 Caleosin related protein Carb_anhydrase PF00194.12 −105 Eukaryotic-type carbonic anhydrase Carboxyl_trans PF01039.13 −262.3 Carboxyl transferase domain Cellulose_synt PF03552.5  −257.9 Cellulose synthase Cenp-O PF09496.1  25 Cenp-O kinetochore centromere component Chal_sti_synt_C PF02797.6  −6.1 Chaicone and stilbene synthases, C-terminal domain Chalcone PF02431.6  25 Chalcone-flavanone isomerase ClpS PF02617.8  −15 ATP-dependent Clp protease adaptor protein ClpS Copine PF07002.7  −36.5 Copine Cu-oxidase PF00394.13 −18.9 Multicopper oxidase Cu-oxidase_2 PF07731.5  −5.8 Multicopper oxidase Cu-oxidase_3 PF07732.6  10 Multicopper oxidase Cullin PF00888.13 −33.3 Cullin family Cupin_1 PF00190.13 −13 Cupin Cupin_2 PF07883.2  19.4 Cupin domain Cyclase PF04199.4  −31.7 Putative cyclase Cyclin_C PF02984.10 −13 Cyclin, C-terminal domain Cyclin_N PF00134.14 −14.7 Cyclin, N-terminal domain DAD PF02109.7  25 DAD family DAO PF01266.15 −34.9 FAD dependent oxidoreductase DCP1 PF06058.4  −16.8 Dcp1-like decapping family DEAD PF00270.20 7.2 DEAD/DEAH box helicase DEK_C PF08766.2  25 DEK C terminal domain DHBP_synthase PF00926.10 −95.1 3,4-dihydroxy-2-butanone 4-phosphate synthase DMRL_synthase PF00885.10 −43 6,7-dimethyl-8-ribityllumazine synthase DREPP PF05558.3  25 DREPP plasma membrane polypeptide DSPc PF00782.11 −21.8 Dual specificity phosphatase, catalytic domain DUF1279 PF06916.4  25 Protein of unknown function (DUF1279) DUF1350 PF07082.2  −145.7 Protein of unknown function (DUF1350) DUF1475 PF07343.2  25 Protein of unknown function (DUF1475) DUF1517 PF07466.2  25 Protein of unknown function (DUF1517) DUF163 PF02590.8  −48.6 Uncharacterized ACR, COG1576 DUF1637 PF07847.3  25 Protein of unknown function (DUF1637) DUF167 PF02594.7  −3.4 Uncharacterised ACR, YggU family COG1872 DUF177 PF02620.8  25 Uncharacterized ACR, COG1399 DUF220 PF02713.5  25 Domain of unknown function DUF220 DUF231 PF03005.6  −58 Arabidopsis proteins of unknown function DUF260 PF03195.5  0.8 Protein of unknown function DUF260 DUF423 PF04241.6  −17.6 Protein of unknown function (DUF423) DUF543 PF04418.3  25 Domain of unknown function (DUF543) DUF569 PF04601.4  −47.6 Protein of unknown function (DUF569) DUF579 PF04669.4  25 Protein of unknown function (DUF579) DUF584 PF04520.4  25 Protein of unknown function, DUF584 DUF588 PF04535.3  25 Domain of unknown function (DUF588) DUF59 PF01883.10 −7.9 Domain of unknown function DUF59 DUF594 PF04578.4  25 Protein of unknown function, DUF594 DUF599 PF04654.3  25 Protein of unknown function, DUF599 DUF6 PF00892.11 21.7 Integral membrane protein DUF6 DUF607 PF04678.4  25 Protein of unknown function, DUF607 DUF616 PF04765.4  25 Protein of unknown function (DUF616) DUF620 PF04788.3  25 Protein of unknown function (DUF620) DUF641 PF04859.3  25 Plant protein of unknown function (DUF641) DUF663 PF04950.3  25 Protein of unknown function (DUF663) DUF822 PF05687.4  25 Plant protein of unknown function (DUF822) DUF829 PF05705.5  25 Eukaryotic protein of unknown function (DUF829) DUF862 PF05903.5  −21.4 PPPDE putative peptidase domain DUF866 PF05907.4  30.1 Eukaryotic protein of unknown function (DUF866) DUF887 PF05967.2  −72.3 Eukaryotic protein of unknown function (DUF887) DUF89 PF01937.10 −113.8 Protein of unknown function DUF89 DUF933 PF06071.4  20 Protein of unknown function (DUF933) DZC PF08381.2  15.3 Disease resistance/zinc finger/chromosome condensation-like region Di19 PF05605.3  25 Drought induced 19 protein (Di19) Dimerisation PF08100.2  25 Dimerisation domain DnaJ PF00226.22 −8 DnaJ domaint Dus PF01207.8  −82.1 Dihydrouridine synthase (Dus) E3_binding PF02817.8  10 e3 binding domain EB1 PF03271.8  25 EB1-like C-terminal motif ECH PF00378.11 −57.6 Enoyl-CoA hydratase/isomerase family ELFV_dehydrog PF00208.12 −26.4 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase ELFV_dehydrog_N PF02812.9  31.8 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain EMP24_GP25L PF01105.15 10.4 emp24/gp25L/p24 family/GOLD ENOD93 PF03386.5  25 Early nodulin 93 ENOD93 protein ENT PF03735.5  25 ENT domain Enolase_C PF00113.13 −71.2 Enolase, C-terminal TIM barrel domain Enolase_N PF03952.7  11.3 Enolase, N-terminal domain Epimerase PF01370.12 −46.3 NAD dependent epimerase/dehydratase family Exo_endo_phos PF03372.14 11 Endonuclease/Exonuclease/phosphatase family F-box PF00646.24 14.4 F-box domain F420_oxidored PF03807.8  −34.5 NADP oxidoreductase coenzyme F420-dependent FAD_binding_2 PF00890.15 −124.8 FAD binding domain FAD_binding_3 PF01494.10 −136.6 FAD binding domain FAE1_CUT1_RppA PF08392.3  −192.7 FAE1/Type III polyketide synthase-like protein FA_hydroxylase PF04116.4  −15.3 Fatty acid hydroxylase superfamily FBA_1 PF07734.4  −39.4 F-box associated FBPase PF00316.11 −170.3 Fructose-1-6-bisphosphatase FHA PF00498.17 25 FHA domain FMO-like PF00743.10 −381.6 Flavin-binding monooxygenase-like FYVE PF01363.12 28.5 FYVE zinc finger Fcf1 PF04900.3  −7.6 Fcf1 Fer2 PF00111.18 7 2Fe-2S iron-sulfur cluster binding domain FolB PF02152.9  25 Dihydroneopterin aldolase Fructosamin_kin PF03881.5  −125.6 Fructosamine kinase G-alpha PF00503.11 −230 G-protein alpha subunit G-patch PF01585.14 18.4 G-patch domain G6PD_C PF02781.7  −175 Glucose-6-phosphate dehydrogenase, C-terminal domain G6PD_N PF00479.13 −99 Glucose-6-phosphate dehydrogenase, NAD binding domain GASA PF02704.5  25 Gibberellin regulated protein GAT PF03127.5  −7 GAT domain GATase PF00117.19 −38.1 Glutamine amidotransferase class-I GFA PF04828.5  12.4 Glutathione-dependent formaldehyde-activating enzyme GH3 PF03321.4  −336 GH3 auxin-responsive promoter GHMP_kinases_C PF08544.4  20.8 GHMP kinases C terminal GHMP_kinases_N PF00288.17 17.1 GHMP kinases N terminal domain GIDA PF01134.13 −226.7 Glucose inhibited division protein A GLTP PF08718.2  −71.1 Glycolipid transfer protein (GLTP) GMP_synt_C PF00958.13 25 GMP synthase C terminal domain GST_C PF00043.16 22.3 Glutathione S-transferase, C-terminal domain GST_N PF02798.11 14.6 Glutathione S-transferase, N-terminal domain GTP_cyclohydro2 PF00925.11 −49 GTP cyclohydrolase II G_glu_transpept PF01019.12 −236.1 Gamma-glutamyltranspeptidase Gln-synt_C PF00120.15 −124 Glutamine synthetase, catalytic domain GlutR_N PF05201.6  −37.8 Glutamyl-tRNAGlu reductase, N-terminal domain GlutR_dimer PF00745.11 25 Glutamyl-tRNAGlu reductase, dimerisation domain Glutaminase PF04960.6  −143.6 Glutaminase Glutaredoxin PF00462.15 17.2 Glutaredoxin Glyco_tran_28_C PF04101.7  −10.4 Glycosyltransferase family 28 C-terminal domain Glyco_transf_29 PF00777.9  −74 Glycosyltransferase family 29 (sialyltransferase) Glyco_transf_8 PF01501.11 −43.2 Glycosyl transferase family 8 Glycolytic PF00274.10 −174.5 Fructose-bisphosphate aldolase class-I Glycos_transf_1 PF00534.11 −7.3 Glycosyl transferases group 1 Glyoxalase PF00903.16 12.1 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily Gp_dh_C PF02800.11 −64.1 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain Gp_dh_N PF00044.15 −74.2 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain HI0933_like PF03486.5  −255.8 HI0933-like protein H_PPase PF03030.7  −377 Inorganic H+ pyrophosphatase Helicase_C PF00271.22 2.4 Helicase conserved C-terminal domain Hep_59 PF07052.2  25 Hepatocellular carcinoma-associated antigen 59 Hexapep PF00132.15 0.3 Bacterial transferase hexapeptide (three repeats) Hin1 PF07320.4  25 Harpin-induced protein 1 (Hin1) His_biosynth PF00977.12 −102.4 Histidine biosynthesis protein Histone PF00125.15 17.4 Core histone H2A/H2B/H3/H4 Hpt PF01627.14 25 Hpt domain Hydrolase PF00702.17 13.6 haloacid dehalogenase-like hydrolase IF4E PF01652.9  −35 Eukaryotic initiation factor 4E IQ PF00612.18 11.9 IQ calmodulin-binding motif IU_nue_hydro PF01156.10 −154 Inosine-uridine preferring nucleoside hydrolase Inositol_P PF00459.16 −55.6 Inositol monophosphatase family Invertase_neut PF04853.3  −233.6 Plant neutral invertase Ion_trans_2 PF07885.7  24.9 Ion channel Iso_dh PF00180.11 −97 Isocitrate/isopropylmalate dehydrogenase KH_1 PF00013.20 12.5 KH domain KH_2 PF07650.8  5 KH domain KR PF08659.1  −74.3 KR domain Kelch_1 PF01344.16 11.7 Kelch motif Kelch_2 PF07646.6  14 Kelch motif LAG1 PF03798.7  −57.5 Longevity-assurance protein (LAG1) LANC_like PF05147.4  −76.9 Lanthionine synthetase C-like protein LEA_5 PF00477.8  25 Small hydrophilic plant seed protein LRRNT_2 PF08263.3  18.6 Leucine rich repeat N-terminal domain LRR_1 PF00560.24 7.7 Leucine Rich Repeat LRR_2 PF07723.4  6 Leucine Rich Repeat LSM PF01423.13 13.7 LSM domain La PF05383.8  25 La domain Lectin_legB PF00139.10 −110.1 Legume lectin domain Ligase_CoA PF00549.10 −43.3 CoA-ligase Lipase_3 PF01764.16 −8 Lipase (class 3) MACPF PF01823.10 −24.6 MAC/Perforin domain MATH PF00917.17 0.5 MATH domain MFS_1 PF07690.7  23.5 Major Facilitator Superfamily MIP PF00230.11 −62 Major intrinsic protein MMR_HSR1 PF01926.14 31.2 GTPase of unknown function MOSC PF03473.8  25 MOSC domain MOSC_N PF03476.7  25 MOSC N-terminal beta barrel domain MT-A70 PF05063.5  −40.8 MT-A70 Malic_M PF03949.6  −143.9 Malic enzyme, NAD binding domain MannoseP_isomer PF01050.9  −70 Mannose-6-phosphate isomerase Mem_trans PF03547.9  −73.4 Membrane transport protein Metalloenzyme PF01676.9  −14.4 Metalloenzyme superfamily Metallophos PF00149.19 22 Calcineurin-like phosphoesterase Methyltransf_11 PF08241.3  21 Methyltransferase domain Methyltransf_12 PF08242.3  23 Methyltransferase domain Methyltransf_2 PF00891.9  −103.8 O-methyltransferase Miro PF08477.4  10.8 Miro-like protein Mito_carr PF00153.18 0 Mitochondrial carrier protein Mov34 PF01398.12 0.9 Mov34/MPN/PAD-1 family MtN3_slv PF03083.7  9.7 MtN3/saliva family NAC PF01849.9  0 NAC domain NAD_Gly3P_dh_C PF07479.5  −50.8 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus NAD_Gly3P_dh_N PF01210.14 −44 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus NAD_binding_2 PF03446.6  −63.5 NAD binding domain of 6-phosphogluconate dehydrogenase NAD_binding_4 PF07993.3  −87.7 Male sterility protein NAF PF03822.5  4.5 NAF domain NAP PF00956.9  −122 Nucleosome assembly protein (NAP) NDK PF00334.10 −59.9 Nucleoside diphosphate kinase NHL PF01436.12 3.8 NHL repeat NIR_SIR PF01077.13 −19.6 Nitrite and sulphite reductase 4Fe-4S domain NIR_SIR_ferr PF03460.8  2.4 Nitrite/Sulfite reductase ferredoxin-like half domain NOI PF05627.2  0.3 Nitrate-induced NOI protein NOSIC PF08060.4  25 NOSIC (NUC001) domain NPH3 PF03000.5  25 NPH3 family NTF2 PF02136.11 6 Nuclear transport factor 2 (NTF2) domain NTP_transferase PF00483.14 −39.9 Nucleotidyl transferase Na_Ca_ex PF01699.15 25 Sodium/calcium exchanger protein Na_H_Exchanger PF00999.12 −67.9 Sodium/hydrogen exchanger family Na_sulph_symp PF00939.10 −259 Sodium:sulfate symporter transmembrane region Nfu_N PF08712.2  20 Scaffold protein Nfu/NifU N terminal NifU PF01106.8  −5.6 NifU-like domain NifU_N PF01592.7  −27.4 NifU-like N terminal domain Nodulin-like PF06813.4  −57.8 Nodulin-like Nop PF01798.9  25 Putative snoRNA binding domain Nramp PF01566.9  −171.4 Natural resistance-associated macrophage protein OPT PF03169.6  −238.6 OPT oligopeptide transporter protein ORC2 PF04084.5  −181.2 Origin recognition complex subunit 2 OTCace PF00185.15 −42 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain OTCace_N PF02729.12 −55 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain PA PF02225.13 13 PA domain PAD_porph PF04371.6  −180.8 Porphyromonas-type peptidyl-arginine deiminase PALP PF00291.16 −70 Pyridoxal-phosphate dependent enzyme PAN_1 PF00024.17 1.4 PAN domain PAN_2 PF08276.2  −4.9 PAN-like domain PAP_fibrillin PF04755.3  25 PAP_fibrillin PB1 PF00564.15 12.3 PB1 domain PCI PF01399.18 25 PCI domain PDCD2_C PF04194.4  −40.9 Programmed cell death protein 2, C-terminal putative domain PDT PF00800.9  25 Prephenate dehydratase PEP-utilizers PF00391.14 0.6 PEP-utilising enzyme, mobile domain PEP-utilizers_C PF02896.9  −173 PEP-utilising enzyme, TIM barrel domain PGAM PF00300.13 −3 Phosphoglycerate mutase family PGI PF00342.10 −168.9 Phosphoglucose isomerase PGK PF00162.10 −39.3 Phosphoglycerate kinase PH PF00169.20 25.1 PH domain PHD PF00628.20 26.2 PHD-finger PI-PLC-X PF00388.10 18.8 Phosphatidylinositol-specific phospholipase C, X domain PI-PLC-Y PF00387.10 −11 Phosphatidylinositol-specific phospholipase C, Y domain PK PF00224.12 −244 Pyruvate kinase, barrel domain PK_C PF02887.7  −44 Pyruvate kinase, alpha/beta domain PLAC8 PF04749.8  −1.1 PLAC8 family PMEI PF04043.6  25 Plant invertase/pectin methylesterase inhibitor PP-binding PF00550.16 25.3 Phosphopantetheine attachment site PP2C PF00481.12 −36.3 Protein phosphatase 2C PPDK_N PF01326.10 −150.2 Pyruvate phosphate dikinase, PEP/pyruvate binding domain PPR PF01535.11 0 PPR repeat PRA1 PF03208.10 25 PRA1 family protein PRC PF05239.7  25 PRC-barrel domain PRK PF00485.9  −28.5 Phosphoribulokinase/Uridine kinase family PRMT5 PF05185.7  25 PRMT5 arginine-N-methyltransferase PTA_PTB PF01515.10 −165.5 Phosphate acetyl/butaryl transferase PTPA PF03095.6  −106 Phosphotyrosyl phosphate activator (PTPA) protein PTR2 PF00854.12 −50 POT family PTS_2-RNA PF01885.7  −48 RNA 2′-phosphotransferase, Tpt1/KptA family Pentapeptide PF00805.13 0 Pentapeptide repeats (8 copies) Peptidase_C12 PF01088.12 10 Ubiquitin carboxyl-terminal hydrolase, family 1 Peptidase_C14 PF00656.13 −22.5 Caspase domain Peptidase_C48 PF02902.10 −13.1 Ulp1 protease family, C-terminal catalytic domain Peptidase_M16 PF00675.11 −38 Insulinase (Peptidase family M16) Peptidase_M16_C PF05193.12 7.9 Peptidase M16 inactive domain Peptidase_M18 PF02127.6  −250.8 Aminopeptidase I zinc metalloprotease (M18) Peptidase_M24 PF00557.15 −70.7 metallopeptidase family M24 Peptidase_S8 PF00082.13 −51 Subtilase family Per1 PF04080.4  25 Per1-like Pescadillo_N PF06732.2  −167.1 Pescadillo N-terminus PfkB PF00294.15 −67.8 pfkB family carbohydrate kinase PhzC-PhzF PF02567.7  −66 Phenazine biosynthesis-like protein Pkinase PF00069.16 70.3 Protein kinase domain Pkinase_C PF00433.15 14.1 Protein kinase C terminal domain Pkinase_Tyr PF07714.8  65 Protein tyrosine kinase Polysacc_synt_2 PF02719.6  −176 Polysaccharide biosynthesis protein Porin_3 PF01459.13 −53 Eukaryotic porin Pre-SET PF05033.7  3.9 Pre-SET motif Pribosyltran PF00156.18 2 Phosphoribosyl transferase domain Pro_isomerase PF00160.12 −37 Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD Proteasome PF00227.17 −36.7 Proteasome A-type and B-type PsbW PF07123.3  6.7 Photosystem II reaction centre W protein (PsbW) Pyr_redox PF00070.18 5 Pyridine nucleotide-disulphide oxidoreductase Pyr_redox_2 PF07992.5  −20 Pyridine nucleotide-disulphide oxidoreductase Pyr_redox_dim PF02852.13 −13 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain Pyridoxal_deC PF00282.10 −158.6 Pyridoxal-dependent decarboxylase conserved domain Pyrophosphatase PF00719.10 −41 Inorganic pyrophosphatase RALF PF05498.2  25 Rapid ALkalinization Factor (RALF) RAMP4 PF06624.3  25 Ribosome associated membrane protein RAMP4 RCC1 PF00415.9  21.2 Regulator of chromosome condensation (RCC1) RNA_pol_I_A49 PF06870.3  25 A49-like RNA polymerase I associated factor RNA_pol_N PF01194.8  25 RNA polymerases N/8 kDa subunit RNA_pol_Rpb5_C PF01191.10 25 RNA polymerase Rpb5, C-terminal domain RNA_pol_Rpb5_N PF03871.5  −8.9 RNA polymerase Rpb5, N-terminal domain RNase_PH PF01138.12 4 3′ exoribonuclease family, domain 1 RNase_PH_C PF03725.6  20 3′ exoribonuclease family, domain 2 RPE65 PF03055.6  −156.5 Retinal pigment epithelial membrane protein RRM_1 PF00076.13 17.7 RNA recognition motif, (a.k.a. RRM, RBD, or RNP domain) RRM_2 PF04059.3  25 RNA recognition motif 2 RRM_3 PF08777.2  0.5 RNA binding motif RRS1 PF04939.3  −60.5 Ribosome biogenesis regulatory protein (RRS1) Raffinose_syn PF05691.3  −395.7 Raffinose synthase or seed imbibition protein Sip1 Ras PF00071.13 −69.9 Ras family Redoxin PF08534.1  −1 Redoxin Rep_fac_C PF08542.2  −0.4 Replication factor C Response_reg PF00072.15 4 Response regulator receiver domain Rho_GDI PF02115.8  −55 RHO protein GDP dissociation inhibitor Rhodanese PF00581.11 25 Rhodanese-like domain Rib_5-P_isom_A PF06026.5  −84.5 Ribose 5-phosphate isomerase A (phosphoriboisomerase A) Ribosomal_L12 PF00542.10 25 Ribosomal protein L7/L12 C-terminal domain Ribosomal_L7Ae PF01248.17 6 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family Ribosomal_S5 PF00333.11 25 Ribosomal protein S5, N-terminal domain Ribosomal_S5_C PF03719.6  0 Ribosomal protein S5, C-terminal domain Ribosomal_S6e PF01092.10 25 Ribosomal protein S6e Ribul_P_3_epim PF00834.10 −97.3 Ribulose-phosphate 3 epimerase family Rick_17kDa_Anti PF05433.6  23.2 Rickettsia 17 kDa surface antigen RmID_sub_bind PF04321.8  −171.8 RmID substrate binding domain SAM_1 PF00536.21 11.3 SAM domain (Sterile alpha motif) SAM_2 PF07647.8  0 SAM domain (Sterile alpha motif) SATase_N PF06426.5  25 Serine acetyltransferase, N-terminal SBF PF01758.7  −27.8 Sodium Bile acid symporter family SET PF00856.19 23.5 SET domain SFT2 PF07770.3  −14.4 SFT2-like protein SH3_1 PF00018.19 −8 SH3 domain SH3_2 PF07653.8  0 Variant SH3 domain SIP1 PF04938.3  25 Survival motor neuron (SMN) interacting protein 1 (SIP1) SMP PF04927.3  25 Seed maturation protein SNARE PF05739.10 23.8 SNARE domain SNF5 PF04855.3  25 SNF5/SMARCB1/INI1 SQS_PSY PF00494.10 −78 Squalene/phytoene synthase SRF-TF PF00319.9  11 SRF-type transcription factor (DNA-binding and dimerisation domain) SRPRB PF09439.1  −45.6 Signal recognition particle receptor beta subunit SSB PF00436.16 0.4 Single-strand binding protein family STAS PF01740.12 0 STAS domain STT3 PF02516.5  −175 Oligosaccharyl transferase STT3 subunit SWIB PF02201.9  −5.7 SWIB/MDM2 domain SYF2 PF08231.3  25 SYF2 splicing factor S_locus_glycop PF00954.11 −12.7 S-locus glycoprotein family Sad1_UNC PF07738.4  −20.4 Sad1/UNC-like C-terminal Sec1 PF00995.14 −272 Sec1 family Sec61_beta PF03911.7  25 Sec61beta family Sedlin_N PF04628.4  −22.1 Sedlin, N-terminal conserved region SeIR PF01641.9  −66.5 SeIR domain Shikimate_DH PF01488.11 −4.4 Shikimate/quinate 5-dehydrogenase Sina PF03145.7  −48.4 Seven in absentia protein family Skp1 PF01466.10 −2 Skp1 family, dimerisation domain Skp1_POZ PF03931.6  14.9 Skp1 family, tetramerisation domain Smg4_UPF3 PF03467.6  −27.5 Smg-4/UPF3 family Snf7 PF03357.12 −22.9 Snf7 Spc97_Spc98 PF04130.4  −136.8 Spc97/Spe98 family Steroid_dh PF02544.7  −44.7 3-oxo-5-alpha-steroid 4-dehydrogenase Str_synth PF03088.7  4.7 Strictosidine synthase Subtilisin_N PF05922.7  26.1 Subtilisin N-terminal Region Suc_Fer-like PF06999.3  −42.4 Sucrase/ferredoxin-like Sugar_tr PF00083.15 −85 Sugar (and other) transporter Sulfate_transp PF00916.11 −131.5 Sulfate transporter family Sybindin PF04099.3  −44.4 Sybindin-like family Synaptobrevin PF00957.12 25 Synaptobrevin Syntaxin PF00804.16 11.4 Syntaxin TATA_RF PF08612.2  25 TATA-binding related factor (TRF) TB2_DP1_HVA22 PF03134.10 −6.9 TB2/DP1, HVA22 family TBC PF00566.9  −58 TBC domain TBP PF00352.12 −8 Transcription factor TFIID (or TATA-binding protein, TBP) TFIID-18kDa PF02269.7  −7.3 Transcription initiation factor IID, 18kD subunit TFIID-31kDa PF02291.6  25 Transcription initiation factor IID, 31kD subunit TFIID_30kDa PF03540.4  25 Transcription initiation factor TFIID 23-30kDa subunit TIM PF00121.9  −97 Triosephosphate isomerase TLC PF03219.5  25 TLC ATP/ADP transporter TPP_enzyme_C PF02775.12 19.7 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain TPP_enzyme_M PF00205.13 −8.1 Thiamine pyrophosphate enzyme, central domain TPP_enzyme_N PF02776.9  −70 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain TPT PF03151.7  −15.3 Triose-phosphate Transporter family Tbf5 PF06331.3  25 Transcription factor TFIIH complex subunit Tfb5 Tetraspannin PF00335.11 −15.4 Tetraspanin family ThiF PF00899.12 −38.4 ThiF family Thioredoxin PF00085.11 −25.7 Thioredoxin Thr_dehydrat_C PF00585.9  −7.9 C-terminal regulatory domain of Threonine dehydratase Transket_pyr PF02779.15 −49 Transketolase, pyrimidine binding domain Transketolase_C PF02780.11 −15.5 Transketolase, C-terminal domain TrkA_C PF02080.12 25 TrkA-C domain TrkA_N PF02254.9  4.7 TrkA-N domain Tryp_alpha_amyl PF00234.13 −0.2 Protease inhibitor/seed storage/LTP family Tyr-DNA_phospho PF06087.3  −152.8 Tyrosyl-DNA phosphodiesterase U-box PF04564.6  −7.6 U-box domain U3_snoRNA_C PF09384.1  25 U3 small nucleolar RNA C terminal UBA PF00627.22 20.7 UBA/TS-N domain UBX PF00789.11 10 UBX domain UDPG_MGDP_dh PF00984.10 −6.9 UDP-glucose/GDP-mannose dehydrogenase family, central domain UDPG_MGDP_dh_C PF03720.6  0.8 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain UDPG_MGDP_dh_N PF03721.5  −74.8 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain UIM PF02809.11 16.6 Ubiquitin interaction motif UPF0061 PF02696.5  −200 Uncharacterized ACR, YdiU/UPF0061 family UPF0139 PF03669.4  25 Uncharacterised protein family (UPF0139) UPF0153 PF03692.6  11.7 Uncharacterised protein family (UPF0153) UPF0185 PF03671.5  11.6 Uncharacterised protein family (UPF0185) UQ_con PF00179.17 −30 Ubiquitin-conjugating enzyme Ubie_methyltran PF01209.9  −117 ubiE/COQ5 methyltransferase family Usp PF00582.17 21.6 Universal stress protein family V-ATPase_G PF03179.6  −19.8 Vacuolar (H+)-ATPase G subunit VHS PF00790.10 −13.2 VHS domain VQ PF05678.5  25 VQ motif WAK PF08488.2  25 Wall-associated kinase WD40 PF00400.23 21.5 WD domain, G-beta repeat Whi5 PF08528.2  25 Whi5 like X8 PF07983.4  −28.8 X8 domain XH PF03469.5  25 XH domain XS PF03468.5  25 XS domain YDG_SRA PF02182.8  25 YDG/SRA domain YIF1 PF03878.6  −81.2 YIF1 YTH PF04146.6  25 YT521-B-like family Y_phosphatase2 PF03162.4  −47.6 Tyrosine phosphatase family YgbB PF02542.7  25 YgbB family Zip PF02535.13 −25.6 ZIP Zinc transporter adh_short PF00106.16 −40.2 short chain dehydrogenase dsrm PF00035.16 24.6 Double-stranded RNA binding motif eIF2A PF08662.2  0 Eukaryotic translation initiation factor eIF2A eIF3_subunit PF08597.1  11.9 Translation initiation factor eIF3 subunit efhand PF00036.23 21.7 EF hand efhand_like PF09279.2  8.8 Phosphoinositide-specific phospholipase C, efhand-like iPGM_N PF06415.4  −263.4 BPG-independent PGAM N-terminus (iPGM_N) mTERF PF02536.5  −60 mTERF malic PF00390.10 25 Malic enzyme, N-terminal domain p450 PF00067.13 −105 Cytochrome P450 peroxidase PF00141.14 −10 Peroxidase polyprenyl_synt PF00348.8  −43 Polyprenyl synthetase tRNA-synt_1c PF00749.12 −130.2 tRNA synthetases class I (E and Q), catalytic domain tRNA-synt_1c_C PF03950.9  25 tRNA synthetases class I (E and Q), anti-codon binding domain zf-A20 PF01754.7  25 A20-like zinc finger zf-AN1 PF01428.7  0 AN1-like Zinc finger zf-C2H2 PF00096.17 17.7 Zinc finger, C2H2 type zf-C3HC4 PF00097.16 16 Zinc finger, C3HC4 type (RING finger) zf-CCCH PF00642.15 0 Zinc finger C-x8-C-x5-C-x3-H type (and similar) zf-CCHC PF00098.14 17.9 Zinc knuckle zf-DHHC PF01529.11 −11 DHHC zinc finger domain zf-MYND PF01753.9  11 MYND finger zf-Tim10_DDP PF02953.6  −5 Tim10/DDP family zinc finger

Example 10 Selection of Transgenic Plants with Enhanced Agronomic Trait(s)

This example illustrates identification of plant cells of the invention by screening derived plants and seeds for enhanced trait. Transgenic seed and plants in corn, soybean, cotton or canola with recombinant DNA identified in Table 2 are prepared by plant cells transformed with DNA that is stably integrated into the genome of the corn cell. Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as compared to control plants

A. Selection for Enhanced Nitrogen Use Efficiency

Transgenic corn seeds provided by the present invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, e.g. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). A variety of physiological traits are monitored. Plants with enhanced NUE provide higher yield as compared to control plants.

B. Selection for Increased Yield

Effective selection of enhanced yielding transgenic plants uses hybrid progeny of the transgenic plants for corn, cotton, and canola, or inbred progeny of transgenic plants for soybean plants plant such as corn, cotton, canola, or inbred plant such as soy, canola and cotton cotton over multiple locations with plants grown under optimal production management practices, and maximum pest control. A target for improved yield is about a 5% to 10% increase or more in yield as compared to yield produced by plants grown from seed for a control plant. Selection methods can be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons, to statistically distinguish yield improvement from natural environmental effects.

C. Selection for Enhanced Water Use Efficiency (WUE)

The selection process imposes a water withholding period to induce stress drought followed by watering. For for example, for corn, a selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle. The primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment.

D. Selection for Growth Under Cold Stress

(1) Cold germination assay—Trays of transgenic and control seeds are placed in a growth chamber at 9.7° C. for 24 days (no light). Seeds having higher germination rates as compared to the control are identified.

(2) Cold field efficacy trial—A cold field efficacy trial is used to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers begin to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.

Seed emergence is defined as the point when the growing shoot breaks the soil surface. The number of emerged seedlings in each plot is counted everyday from the day the earliest plot begins to emerge until no significant changes in emergence occur. In addition, for each planting date, the latest date when emergence is 0 in all plots is also recorded. Seedling vigor is also rated at V3-V4 stage before the average of corn plant height reaches 10 inches, with 1=excellent early growth, 5=Average growth and 9=poor growth. Days to 50% emergence, maximum percent emergence and seedling vigor are used to determine plants with enhanced cold tolerance.

E. Screens for Transgenic Plant Seeds with Increased Protein and/or Oil Levels

This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample (Table 26). Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan. An NIR calibration for the analytes of interest is used to predict the values of an unknown sample. The NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides predicted values as well as information on how well the sample fits in the calibration.

Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are performed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.

TABLE 23 Typical sample(s): Whole grain corn and soybean seeds Analytical time to run method: Less than 0.75 min per sample Total elapsed time per run: 1.5 minute per sample Typical and minimum Corn typical: 50 cc; minimum 30 cc sample size: Soybean typical: 50 cc; minimum 5 cc Typical analytical range: Determined in part by the specific calibration. Corn - moisture 5-15%, oil 5-20%, protein 5-30%, starch 50-75%, and density 1.0-1.3%. Soybean - moisture 5-15%, oil 15-25%, and protein 35-50%.

Example 11 Cotton Transgenic Plants with Enhanced Agronomic Traits

Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797. Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 803 are obtained by transforming with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants. Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, e.g. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g., irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of −14 to −18 bars, and growing a second set of transgenic and control plants under “dry” conditions, to e.g. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.

The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.

Example 12 Canola Plants with Enhanced Agrominic Traits

This example illustrates plant transformation in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

Tissues from in vitro grown canola seedlings are prepared and inoculated with a suspension of overnight grown Agrobacterium containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium, the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterizations are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants. Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant

Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

Example 13 Selection of Transgenic Plants with Enhanced Agronomic Trait(s)

This example illustrates the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention where the plants and seed are identified by screening for a transgenic plant having an enhanced agronomic trait imparted by expression or suppression of a protein selected from the group including the homologous proteins identified in Example 7. Transgenic plant cells of corn, soybean, cotton, canola, alfalfa, wheat and rice are transformed with recombinant DNA for expressing or suppressing each of the homologs identified in Example 7. Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression or suppression of the homologous proteins.

Example 14 Monocot and Dicot Plant Transformation for the Suppression of Endogeneous Protein

This example illustrates monocot and dicot plant transformation to produce nuclei of this invention in cells of a transgenic plant by transformation where the recombinant DNA suppresses the expression of an endogenous protein identified in Table 24.

Corn, soybean, cotton, or canola tissue are transformed as described in Examples 2-5 using recombinant DNA in the nucleus with DNA that is transcribed into RNA that forms double-stranded RNA targeted to an endogenous gene with DNA encoding the protein. The genes for which the double-stranded RNAs are targeted are the native gene in corn, soybean, cotton or canola that are homologs of the genes encoding the protein that has the function of the protein of Arabidopsis thaliana as identified in Table 24.

Populations of transgenic plants prepared in Examples 3, 4, 5, 6, or 13 with DNA for suppressing a gene identified in Table 2 as providing an enhanced trait by gene suppression are screened to identify an event from those plants with a nucleus of the invention by selecting the trait identified in this specification.

TABLE 24 PEP SEQ Construct ID Pfam module ID Traits 115 AP2 10177 LN 116 zf-C2H2 12155 CS SS 118 F-box::Tub 11873 LN PEG 154 Pex2_Pex12::zf-C3HC4 11113 CS 188 Myb_DNA-binding::Myb_DNA- 12325 LN binding 200 bZIP_1 71228 CK 

What is claimed is:
 1. A plant cell nucleus with stably-integrated, recombinant DNA comprising a promoter that is functional in plant cells and that is operably linked to protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module NTP_transferase::Hexapep::Hexapep::Hexapep; wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA in its nuclei and express said protein for an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of to enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
 2. A plant cell nucleus with stably integrated, recombinant DNA, wherein (a) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of Syntaxin::SNARE, Pro_isomerase, Pkinase, ATP-synt_G, Carboxyl_trans, CDC50, GATase::GMP_synt_C, F-box::WD40::WD40::WD40, dsrm::dsrm, Pyr_redox_2::Pyr_redox_dim, WAK::Pkinase, Pkinase_Tyr, PTPA, Biotin_lipoyl::E3_binding::2-oxoacid_dh, AAA, LRRNT_2::LRR_1::LRR_1::LRR_1, PRA1, TIM, YTH, ThiF, Hep_59, Pkinase, PALP::Thr_dehydrat_C::Thr_dehydrat_C, zf-Tim10_DDP, CAF1, Pkinase, Pyr_redox_2::Pyr_redox_dim, Response_reg, Y1F1, NPH3, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase_Tyr, NOI, Fer2, AA_permease, Caleosin, IF4E, Pkinase, Ribul_P_3_epim, F-box::WD40::WD40::WD40::WD40::WD40::WD40, MIP, p450, Ribosomal_S5::Ribosomal_S5_C, Hpt, TBC, Acyltransferase, Epimerase, Pkinase, Dus, SelR, PH, Tyr-DNA_phospho, RRM_1, Pkinase, ECH, SRPRB, DUF599, Pkinase::efhand::efhand::efhand::efhand, ORC2, PMEI, p450, GLTP, Suc_Fer-like, CBS::CBS, ADH_N::ADH_zinc_N, LRRNT_2::LRR_1::LRR_1::LRR_1::Pkinase, F-box, adh_short, polyprenyl_synt, GHMP_kinases_N::GHMP_kinases_C, PsbW, Na_H_Exchanger::TrkA_C, Ribosomal_L12, CDC50, DCP1, Pyr_redox_2::Pyr_redox_dim, Steroid_dh, tRNA-synt_1c::tRNA-synt_1c_C, Cupin_1::Cupin_1, peroxidase, Sugar_tr, Pro_isomerase, Iso_dh, PTS_2-RNA, Aminotran_5, ENOD93, KH_1::KH_1::KH_1::KH_1::KH_1, Mito_carr::Mito_carr::Mito_carr, DUF569::DUF569, C1_2::C1_2::C1_3::C1_2::C1_3::C1_2, DnaJ::zf-C2H2, Aldedh, AAA::Rep_fac_C, DUF641, Aminotran_1_2, TB2_DP1_HVA22, zf-C3HC4, RRM_1::RRM_2, Pkinase, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, Pyr_redox_2, IQ::IQ, SMP::SMP::SMP, AWPM-19, CLP_protease, Pkinase::NAF, PRMT5, PPR::PPR::PPR::PPR::PPR::PPR, Aldedh, ATP-synt_C::ATP-synt_C, adh_short, RCC1::RCC1::RCC1::RCC1::FYVE::DZC, p450, PfkB, PB1, Hexapep::Hexapep::Hexapep::Hexapep, Aminotran_1_2, DUF862, Aldedh, ADH_N::ADH_zinc_N, CDC48_N::AAA::AAA, AA_permease, UQ_con, Mem_trans, GFA, OPT, DUF887, Di19, U-box::Arm::Arm, DAO, G-alpha, Aminotran_3, 2OG-FeII_Oxy, Lectin_legB::Pkinase, NAC::UBA, efhand_like::PI-PLC-X::PI-PLC-Y::C2, TLC, ATP-grasp_2::Ligase_CoA, Pkinase, PRC::PRC, MFS_1::Sugar_tr, Copine::zf-C3HC4, RRM_1::RRM_1::RRM_1, Pribosyltran, AA_kinase, PhzC-PhzF, Gp_dh_N::Gp_dh_C, Sugar_tr, Pre-SET::SET, Alpha-amylase::Alpha-amyl_C2, Cyclin_N, FAE1_CUT1_RppA::ACP_syn_III_C, RPE65, efhand_like::PI-PLC-X::PI-PLC-Y::C2, Mito_carr::Mito_carr::Mito_carr, Invertase_neut, DSPc, LANC_like, Aminotran_5, Glutaminase, PPR..PPR..PPR..PPR..PPR::PPR::PPR::PPR, PGI, SSD, p450, La::RRM_1::RRM_3, Methyltransf_11, SBF, NTP_transferase::Hexapep::Hexapep::Hexapep, Mov34, Hydrolase, AAA, RRM_1::RRM_1, Pkinase::NAF, F-box::FBA_1, p450, F-box::LRR_2, zf-DHHC, TBP::TBP, DUF607, FMO-like, adh_short, ATP-synt_ab_N::ATP-synt_ab, RNase_PH, PP2C, UQ_con, Aminotran_1_2, p450, FMO-like, Gp_dh_N::Gp_dh_C, Mito_carr::Mito_carr::Mito_carr, zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH, GST_C, GH3, PAP_fibrillin, ThiF, Ribul_P_3_epim, DUF260, p450, MACPF, Steroid_dh, Response_reg, Carb_anhydrase, Aldedh, Pkinase, Methyltransf_11, PK::PK_C, Pkinase, DEK_C::SWIB::SWIB, TATA_RF, Tryp_alpha_amyl, Y_phosphatase2, TATA_RF, NifU_N, ENT, Pkinase, F-box::Kelch_2::Kelch_2, WD40::WD40, MtN3_slv::MtN3_slv, TB2_DP1_HVA22, Pkinase, Aldedh, AAA, Pyridoxa1_deC, zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC, Peptidase_M24, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase, Arf, DUF1279, UPF0185, Rhodanese, adh_short, Tryp_alpha_amyl, Pkinase, UPF0139, CBS, Glyco_transf_29, iPGM_N::Metalloenzyme, Proteasome, Pkinase, UBX, ELFV_dehydrog_N::ELFV_dehydrog, p450, ADH_N::ADH_zinc_N, zf-C3HC4, NDK, NAD_Gly3P_dh_N::NAD_Gly3P_dh_C, GlutR_N::Shikimate_DH::GlutR_dimer, p450, SNFS, p450, Pribosyltran, AIG1, Response_reg::CCT, mTERF, DUF220, Pkinase::NAF, zf-CCCH::zf-CCCH, Pkinase, Pkinase, MATH::MATH, Asparaginase, Pkinase, Gp_dh_N::Gp_dh_C, Pkinase, KH_1, Fcf1, PK::PK_C::PEP-utilizers, CRAL_TRIO_N::CRAL_TRIO, Raffinose_syn, DUF584, BT1, Aminotran_1_2, C1_2::C1_3::C1_3::C1_2::C1_3::C1_3::C1_2, FMO-like, PLAC8, F-box::Kelch_2::Kelch_1::Kelch_2, XS::XH, STT3, ABC_tran::ABC_tran, Aldo_ket_red, NTF2::RRM_1, DUF594, Biotin_lipoyl::2-oxoacid_dh, RRM_1, FHA, Mov34, MT-A70, Brix, X8, Auxin_inducible, Peptidase_M18, Sec61_beta, F-box::Kelch_1::Kelch_1, Brix, TIM, CTP_transf_1, Tetraspannin, PALP, DUF822, Pkinase, B3::B3, MFS_1, SFT2, F-box::Kelch_1::Kelch_1, DUF588, Thioredoxin, Alba, Ion_trans_2::Ion_trans_2, Peptidase_C48, YDG_SRA::Pre-SET::SET, Aldedh, Abhydrolase_3, p450, U-box::Arm::Arm::Arm::Arm, AA_permease, LAG1, peroxidase, PAD_porph, Pkinase, F-box, AIG2, p450, AARP2CN::DUF663, UPF0153, NAD_binding_2::6PGD, Pkinase, B_lectin::S_locus_glycop::PAN_1::Pkinase, EMP24_GP25L, DUF6::DUF6, DUF163, Sina, adh_short, Rho_GDI, zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC, VHS::GAT, Pyrophosphatase, DMRL_synthase, Cyclin_N::Cyclin_C, NDK, TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme C, SH3 1, UDPG_MGDP_dh_N::UDPG_MGDP_dh::UDPG_MGDP_dh_C, UIM::efhand, DUF579, Pkinase, DHBP_synthase::GTP_cyclohydro2, Peptidase_C14, Glycolytic, Pkinase, Lipase_3, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1, Snf7, BT1, PPDK_N::PEP-utilizers::PEP-utilizers_C, V-ATPase_G, RNA_pol_I_A49, Zip, WD40::WD40::WD40, Branch, RCC1::RCC1::RCC1::RCC1, TFIID-18kDa, Pkinase, Cullin, TFIID-31kDa, Asp, Pkinase, Ubie_methyltran, PPR::PPR, PPR::PPR::PPR::PPR::PPR::PPR::PPR, Fructosamin_kin, PPR::PPR::PPR::PPR::PPR::PPR, Pkinase_Tyr, p450, AA_permease, Glycos_transf_1, ECH::3HCDH_N::3HCDH, MIP, ADH_N::ADH_zinc_N, Aa_trans, DUF1517, Redoxin, RRS1, Pribosyltran, Sulfate_transp::STAS, DUF167, MMR_HSR1::DUF933, Aminotran_1_2, AA_permease, DUF620, Aldedh, Aminotran_1_2, LRR_1, CDP-OH_P_transf, DHBP_synthase::GTP_cyclohydro2, NHL::NHL, WD40::U3_snoRNA_C, Na_sulph_symp, adh_short, Thioredoxin, Ribosomal_L7Ae, OTCace_N::OTCace, Mito_carr::Mito_carr::Mito_carr, Pescadillo_N::BRCT, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, mTERF, Chalcone, Per1, PPR::PPR, Na_H_Exchanger::TrkA_N, DEAD::Helicase_C, Cyclin_N::Cyclin_C, PP-binding, SRF-TF, SATase_N::Hexapep::Hexapep::Hexapep, PK::PK_C, adh_short, DUF6::DUF6, Pyr_redox_2, G-patch, WD40::WD40::WD40::WD40, G-alpha, VQ, WD40::WD40::WD40::WD40::WD40, Aminotran_3, Pribosyltran, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1, eIF3_subunit, H_PPase, Nodulin-like, Whi5, Tryp_alpha_amyl, NIR_SIR_ferr::NIR_SIR::NIR_SIR_ferr, RRM_1::RRM_1, Band_7, Asp, MFS_1, F420_oxidored, Pkinase, PRK, Na_Ca_ex::Na_Ca_ex, Bombesin, Pkinase, Epimerase, Pkinase, Inositol_P, Arm::Arm::Arm::Arm, PB1, Hin1, p450, RNA_pol_Rpb5_N::RNA_pol_Rpb5_C, Adap_comp_sub, Peptidase_M16::Peptidase_M16_C, Pkinase, PGK, Biotin_lipoyl::E3_binding::2-oxoacid_dh, Alg6_Alg8, F-box, MMR_HSR1, G6PD_N::G6PD_C, DAD, malic::Malic_M::PTA_PTB, ADH_N::ADH_zinc_N, LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1, PfkB, PA, Pyr_redox_2::Pyr_redox_dim, SIP1, PP2C, BT1, AhpC-TSA, GASA, Aminotran_3, Sad1_UNC, Pkinase, zf-MYND::PDCD2_C, Pkinase, PGK, ArfGap, GATase::GMP_synt_C, p450, DUF1637, 2OG-FeII_Oxy, Aldedh, DUF231, Glyco_transf_8, Sec1, DUF1475, Cellulose_synt, RRM_1::RRM_1::RRM_1, Usp, AA_permease, Acetyltransf_1::Bromodomain, Glyco_tran_28_C, RNA_pol_N, NTP_transferase, malic::Malic_M, Histone, Epimerase, UPF0061, ClpS, LEA_5, Auxin_inducible, PAP_fibrillin, Aldo_ket_red, Gln-synt_C, DREPP, p450, SFT2, eIF2A, Cenp-O, CPSase_sm_chain::GATase, WD40::WD40::WD40, Pkinase, Porin_3, Pkinase, Aminotran_1_2, GST_N::GST_C, F-box::Kelch_1::Kelch_1, IU_nuc_hydro, SYF2, PDT, Subtilisin_N::PA, Sugar_tr, WD40::WD40, p450, DUF829, Pyr_redox_2::Pyr_redox_dim, Aminotran_1_2, Cyclin_N::Cyclin_C, YgbB, Sugar_tr, SRF-TF, DUF231, DUF584, BT1, zf-C3HC4, Metallophos, FA_hydroxylase, p450, ACBP::Ank::Ank, LSM, SAM_1, LRR_1::LRR_1::Pkinase, Cullin, F-box::FBA_1, peroxidase, Rib_5-P_isom_A, zf-A20::zf-AN1, Dimerisation::Methyltransf_2, PGAM, PTR2, Copine, PALP, Exo_endo_phos, G6PD_N::G6PD_C, PLAC8, Aldo_ket_red, Ank::Ank, FBPase, zf-C3HC4, ACT::ACT, Suc_Fer-like, Pkinase_Tyr, G-alpha, RAMP4, Glutaredoxin, RRM_1::RRM_1, MT-A70; Response_reg::CCT, Arf, AP2, DUF177, 2OG-FeII_Oxy, LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1, Aldedh, DUF1350, FAE1_CUT1_RppA::ACP_syn_III_C, Sybindin, zf-C3HC4, Nfu_N::NifU, Rho_GDI, PK::PK_C, NOSIC::Nop, PK::PK_C, PRK::Pribosyltran, PfkB, p450, DUF231, TFIID_30kDa, Aldedh, zf-AN1, GHMP_kinases_N::GHMP_kinases_C, DUF423, Pkinase, Cu-oxidase_3::Cu-oxidase::Cu-oxidase_2, PCI, RNase_PH::RNase_PH_C, DUF59, NTP_transferase, CH::EB1, Pkinase::Pkinase_C, DUF866, SMP::SMP::SMP, Aminotran_3, Transket_pyr::Transketolase_C, Copine, His_biosynth, Tbf5, DUF543, p450, C2, DUF616, Gp_dh_N::Gp_dh_C, Smg4_UPF3, DUF231, DUF89, WD40::WD40, Aldedh, ACT::ACT::ACT::ACT, Pkinase, Pyridoxa1_deC, Skp1_POZ::Skp1, NAP, FolB, p450, Pentapeptide::Pentapeptide, NTP_transferase::MannoseP_isomer, SQS_PSY, Cyclase, GASA, Rick_17kDa_Anti, FMO-like, B_lectin::S_locus_glycop::PAN_2, Peptidase_C12, Ribosomal_S6e, Glyoxalase, Response_reg::CCT, PHD::SET, Redoxin, G_glu_transpept, Synaptobrevin, p450, RALF, PALP, Branch, DUF579, Aminotran_3, Nramp, Enolase_N::Enolase_C, Str_synth, FAD_binding_3, MOSC_N::MOSC, Spc97_Spc98, Glycolytic, F-box::WD40::WD40::WD40::WD40, AA_kinase::ACT::ACT, RALF, and ATP_bind_1; (b) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ ID NO: 94617 through 94734; (c) said recombinant DNA comprises a promoter that is functional in plant cells and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence selected from the group consisting of 819, 867, 906, 914, 967, 1009, 1040, 1086, 1107, 1227, 1233, 1250, 1293, 1311, 1320, 1342, 1364, 1365, 1373, 1398, 1402, 1439, 1443, 1473, 1495, 1539, 1596, and homologs thereof listed in table 19; (d) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding recombinant DNA encoding a protein having an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO 1227; (e) said recombinant DNA suppresses comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence comprising a pfam domain module selected from the group consisting of DUF1475, DUF1350, Arm::Arm::Arm::Arm, NifU_N, ATP_bind_1, DUF599, LRR_1, Pyr_redox_2::Pyr_redox_dim, malic::Malic_M, Glycolytic, IF4E, Pkinase, UPF0139, GlutR_N::Shikimate_DH::GlutR_dimer, PLAC8, PLAC8, DUF220, OPT, Glyco_transf_8, Per1, Usp, mTERF, PB1, CAF1, Pkinase, F-box::Kelch_1::Kelch_1, PHD::SET, Nfu_N::NifU, RCC1::RCC1::RCC1::RCC1, X8, Pkinase::NAF, UIM::efhand, Glutaredoxin, DUF1517, Cupin_1::Cupin_1, ClpS, Spc97_Spc98, Subtilisin_N::PA, CBS, PTPA, p450, AA_permease; Sina, p450, Mov34, Thioredoxin, SATase_N::Hexapep::Hexapep::Hexapep, Epimerase, RRM_1::RRM_2, Synaptobrevin, Ribosomal_S6e, Redoxin, MFS_1, PPR::PPR, NPH3, and DUF866; or (f) said recombinant DNA comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence with at least 70% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 811, 813, 819, 891, 893, 909, 911, 1439, 1584, and homologs thereof listed in table 16; and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
 3. The plant cell nucleus of claim 2 wherein said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 804 through SEQ ID NO:
 94613. 4. The plant cell nucleus of claim 2 further comprising DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell.
 5. The plant cell nucleus of claim 4 wherein said herbicide is a glyphosate, dicamba, or glufosinate compound.
 6. A transgenic plant cell or plant comprising a plurality of plant cells with the plant cell nucleus of claim
 2. 7. The transgenic plant cell or plant of claim 6 which is homozygous for said recombinant DNA.
 8. A transgenic seed comprising a plurality of plant cells with a plant cell nucleus of claim
 2. 9. The transgenic seed of claim 8 from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant.
 10. A transgenic pollen grain comprising a haploid derivative of a plant cell nucleus of claim
 2. 11. A method for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of recombinant DNA in a nucleus of claim 2, wherein said method for manufacturing said transgenic seed comprising: (a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil, (b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants, and (c) collecting seeds from selected plant selected from step b.
 12. The method of claim 11 wherein said method for manufacturing said transgenic seed further comprising (a) verifying that said recombinant DNA is stably integrated in said selected plants, and (b) analyzing tissue of said selected plant to determine the expression or suppression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO:804-1606.
 13. The method of claim 11 wherein said seed is corn, soybean, cotton, alfalfa, canola wheat or rice seed.
 14. A method of producing hybrid corn seed comprising: (a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA in a nucleus of claim 2; (b) producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; (c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; (d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; (e) repeating steps (c) and (d) at least once to produce an inbred corn line; and (f) crossing said inbred corn line with a second corn line to produce hybrid seed. 